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1.
J Chem Phys ; 151(4): 044114, 2019 Jul 28.
Artigo em Inglês | MEDLINE | ID: mdl-31370516

RESUMO

We develop a stochastic resolution of identity representation to the second-order Matsubara Green's function (sRI-GF2) theory. Using a stochastic resolution of the Coulomb integrals, the second order Born self-energy in GF2 is decoupled and reduced to matrix products/contractions, which reduces the computational cost from O(N5) to O(N3) (with N being the number of atomic orbitals). The current approach can be viewed as an extension to our previous work on stochastic resolution of identity second order Møller-Plesset perturbation theory [T. Y. Takeshita et al., J. Chem. Theory Comput. 13, 4605 (2017)] and offers an alternative to previous stochastic GF2 formulations [D. Neuhauser et al., J. Chem. Theory Comput. 13, 5396 (2017)]. We show that sRI-GF2 recovers the deterministic GF2 results for small systems, is computationally faster than deterministic GF2 for N > 80, and is a practical approach to describe weak correlations in systems with 103 electrons and more.

2.
J Chem Phys ; 150(4): 044107, 2019 Jan 28.
Artigo em Inglês | MEDLINE | ID: mdl-30709286

RESUMO

Data-driven prediction of molecular properties presents unique challenges to the design of machine learning methods concerning data structure/dimensionality, symmetry adaption, and confidence management. In this paper, we present a kernel-based pipeline that can learn and predict the atomization energy of molecules with high accuracy. The framework employs Gaussian process regression to perform predictions based on the similarity between molecules, which is computed using the marginalized graph kernel. To apply the marginalized graph kernel, a spatial adjacency rule is first employed to convert molecules into graphs whose vertices and edges are labeled by elements and interatomic distances, respectively. We then derive formulas for the efficient evaluation of the kernel. Specific functional components for the marginalized graph kernel are proposed, while the effects of the associated hyperparameters on accuracy and predictive confidence are examined. We show that the graph kernel is particularly suitable for predicting extensive properties because its convolutional structure coincides with that of the covariance formula between sums of random variables. Using an active learning procedure, we demonstrate that the proposed method can achieve a mean absolute error of 0.62 ± 0.01 kcal/mol using as few as 2000 training samples on the QM7 dataset.

3.
Chem Commun (Camb) ; 54(76): 10698-10701, 2018 Sep 20.
Artigo em Inglês | MEDLINE | ID: mdl-30187044

RESUMO

Oxo group activation with reduction of neptunyl(vi) and plutonyl(vi) to tetravalent hydroxo species by the hydroxypyridinone siderophore derivative 3,4,3-LI-(1,2-HOPO) was investigated in the gas-phase via electrospray ionization mass spectrometry, in solution via Raman spectroscopy, and computationally via density functional theory. Dissociation of the gas-phase tetravalent complexes resulted in actinide-hydroxo bond cleavage.

4.
J Chem Phys ; 147(18): 184111, 2017 Nov 14.
Artigo em Inglês | MEDLINE | ID: mdl-29141437

RESUMO

A new large-scale parallel multiconfigurational self-consistent field (MCSCF) implementation in the open-source NWChem computational chemistry code is presented. The generalized active space approach is used to partition large configuration interaction (CI) vectors and generate a sufficient number of batches that can be distributed to the available cores. Massively parallel CI calculations with large active spaces can be performed. The new parallel MCSCF implementation is tested for the chromium trimer and for an active space of 20 electrons in 20 orbitals, which can now routinely be performed. Unprecedented CI calculations with an active space of 22 electrons in 22 orbitals for the pentacene systems were performed and a single CI iteration calculation with an active space of 24 electrons in 24 orbitals for the chromium tetramer was possible. The chromium tetramer corresponds to a CI expansion of one trillion Slater determinants (914 058 513 424) and is the largest conventional CI calculation attempted up to date.

5.
J Phys Chem A ; 121(47): 9156-9162, 2017 Nov 30.
Artigo em Inglês | MEDLINE | ID: mdl-29136367

RESUMO

The highest known actinide oxidation states are Np(VII) and Pu(VII), both of which have been identified in solution and solid compounds. Recently a molecular Np(VII) complex, NpO3(NO3)2-, was prepared and characterized in the gas phase. In accord with the lower stability of heptavalent Pu, no Pu(VII) molecular species has been identified. Reported here are the gas-phase syntheses and characterizations of NpO4- and PuO4-. Reactivity studies and density functional theory computations indicate the heptavalent metal oxidation state in both. This is the first instance of Pu(VII) in the absence of stabilizing effects due to condensed phase solvation or crystal fields. The results indicate that addition of an electron to neutral PuO4, which has a computed electron affinity of 2.56 eV, counterintuitively results in oxidation of Pu(V) to Pu(VII), concomitant with superoxide reduction.

6.
J Cheminform ; 9(1): 55, 2017 Oct 30.
Artigo em Inglês | MEDLINE | ID: mdl-29086154

RESUMO

An end-to-end platform for chemical science research has been developed that integrates data from computational and experimental approaches through a modern web-based interface. The platform offers an interactive visualization and analytics environment that functions well on mobile, laptop and desktop devices. It offers pragmatic solutions to ensure that large and complex data sets are more accessible. Existing desktop applications/frameworks were extended to integrate with high-performance computing resources, and offer command-line tools to automate interaction-connecting distributed teams to this software platform on their own terms. The platform was developed openly, and all source code hosted on the GitHub platform with automated deployment possible using Ansible coupled with standard Ubuntu-based machine images deployed to cloud machines. The platform is designed to enable teams to reap the benefits of the connected web-going beyond what conventional search and analytics platforms offer in this area. It also has the goal of offering federated instances, that can be customized to the sites/research performed. Data gets stored using JSON, extending upon previous approaches using XML, building structures that support computational chemistry calculations. These structures were developed to make it easy to process data across different languages, and send data to a JavaScript-based web client.

7.
Inorg Chem ; 56(21): 12930-12937, 2017 Nov 06.
Artigo em Inglês | MEDLINE | ID: mdl-29019408

RESUMO

Recent efforts to activate the strong uranium-oxygen bonds in the dioxo uranyl cation have been limited to single oxo-group activation through either uranyl reduction and functionalization in solution, or by collision induced dissociation (CID) in the gas-phase, using mass spectrometry (MS). Here, we report and investigate the surprising double activation of uranyl by an organic ligand, 3,4,3-LI(CAM), leading to the formation of a formal U6+ chelate in the gas-phase. The cleavage of both uranyl oxo bonds was experimentally evidenced by CID, using deuterium and 18O isotopic substitutions, and by infrared multiple photon dissociation (IRMPD) spectroscopy. Density functional theory (DFT) computations predict that the overall reaction requires only 132 kJ/mol, with the first oxygen activation entailing about 107 kJ/mol. Combined with analysis of similar, but unreactive ligands, these results shed light on the chelation-driven mechanism of uranyl oxo bond cleavage, demonstrating its dependence on the presence of ligand hydroxyl protons available for direct interactions with the uranyl oxygens.

8.
J Chem Theory Comput ; 13(10): 4605-4610, 2017 Oct 10.
Artigo em Inglês | MEDLINE | ID: mdl-28914534

RESUMO

A stochastic orbital approach to the resolution of identity (RI) approximation for 4-index electron repulsion integrals (ERIs) is presented. The stochastic RI-ERIs are then applied to second order Møller-Plesset perturbation theory (MP2) utilizing a multiple stochastic orbital approach. The introduction of multiple stochastic orbitals results in an O(NAO3) scaling for both the stochastic RI-ERIs and stochastic RI-MP2, NAO being the number of basis functions. For a range of water clusters we demonstrate that this method exhibits a small prefactor and observed scalings of O(Ne2.4) for total energies and O(Ne3.1) for forces (Ne being the number of correlated electrons), outperforming MP2 for clusters with as few as 21 water molecules.

9.
Nat Chem ; 9(9): 843-849, 2017 09.
Artigo em Inglês | MEDLINE | ID: mdl-28837177

RESUMO

Berkelium (Bk) has been predicted to be the only transplutonium element able to exhibit both +III and +IV oxidation states in solution, but evidence of a stable oxidized Bk chelate has so far remained elusive. Here we describe the stabilization of the heaviest 4+ ion of the periodic table, under mild aqueous conditions, using a siderophore derivative. The resulting Bk(IV) complex exhibits luminescence via sensitization through an intramolecular antenna effect. This neutral Bk(IV) coordination compound is not sequestered by the protein siderocalin-a mammalian metal transporter-in contrast to the negatively charged species obtained with neighbouring trivalent actinides americium, curium and californium (Cf). The corresponding Cf(III)-ligand-protein ternary adduct was characterized by X-ray diffraction analysis. Combined with theoretical predictions, these data add significant insight to the field of transplutonium chemistry, and may lead to innovative Bk separation and purification processes.

10.
Inorg Chem ; 56(6): 3686-3694, 2017 Mar 20.
Artigo em Inglês | MEDLINE | ID: mdl-28276685

RESUMO

The synthesis, reactivity, structures, and bonding in gas-phase binary and complex oxide anion molecules of protactinium and uranium have been studied by experiment and theory. The oxalate ions, AnVO2(C2O4)-, where An = Pa or U, are essentially actinyl ions, AnVO2+, coordinated by an oxalate dianion. Both react with water to yield the pentavalent hydroxides, AnVO(OH)2(C2O4)-. The chemistry of Pa and U becomes divergent for reactions that result in oxidation: whereas PaVI is inaccessible, UVI is very stable. The UVO2(C2O4)- complex exhibits a remarkable spontaneous exothermic replacement of the oxalate ligand by O2 to yield UO4- and two CO2 molecules. The structure of the uranium tetroxide anion is computed to correspond to distorted uranyl, UVIO22+, coordinated in the equatorial plane by two equivalent O atoms each having formal charges of -1.5 and U-O bond orders intermediate between single and double. The unreactive nature of PaVO2(C2O4)- toward O2 is a manifestation of the resistance toward oxidation of PaV, and clearly reveals the disparate chemistries of Pa and U. The uranium tetroxide anion, UO4-, reacts with water to yield UO5H2-. Infrared spectra obtained for UO5H2- confirm the computed lowest-energy structure, UO3(OH)2-.

11.
J Phys Chem A ; 120(51): 10216-10222, 2016 Dec 29.
Artigo em Inglês | MEDLINE | ID: mdl-27977185

RESUMO

The presence of counterions in solutions containing highly charged metal cations can trigger processes such as ion-pair formation, hydrogen bond breakages and subsequent re-formation, and ligand exchanges. In this work, it is shown how halide (Cl-, Br-) and perchlorate (ClO4-) anions affect the strength of the primary solvent coordination shells around Th4+ using explicit-solvent and finite-temperature ab initio molecular dynamics modeling methods. The 9-fold solvent geometry was found to be the most stable hydration structure in each aqueous solution. Relative to the dilute aqueous solution, the presence of the counterions did not significantly alter the geometry of the primary hydration shell. However, the free energy analyses indicated that the 10-fold hydrated states were thermodynamically accessible in dilute and bromide aqueous solutions within 1 kcal/mol. Analysis of the results showed that the hydrogen bond lifetimes were longer and solvent exchange energy barriers were larger in solutions with counterions in comparison with the solution with no counterions. This implies that the presence of the counterions induces a strengthening of the Th4+ hydration shell.

12.
J Cheminform ; 8: 8, 2016.
Artigo em Inglês | MEDLINE | ID: mdl-26865863

RESUMO

BACKGROUND: The testing of theoretical models with experimental data is an integral part of the scientific method, and a logical place to search for new ways of stimulating scientific productivity. Often experiment/theory comparisons may be viewed as a workflow comprised of well-defined, rote operations distributed over several distinct computers, as exemplified by the way in which predictions from electronic structure theories are evaluated with results from spectroscopic experiments. For workflows such as this, which may be laborious and time consuming to perform manually, software that could orchestrate the operations and transfer results between computers in a seamless and automated fashion would offer major efficiency gains. Such tools also promise to alter how researchers interact with data outside their field of specialization by, e.g., making raw experimental results more accessible to theorists, and the outputs of theoretical calculations more readily comprehended by experimentalists. RESULTS: An implementation of an automated workflow has been developed for the integrated analysis of data from nuclear magnetic resonance (NMR) experiments and electronic structure calculations. Kepler (Altintas et al. 2004) open source software was used to coordinate the processing and transfer of data at each step of the workflow. This workflow incorporated several open source software components, including electronic structure code to compute NMR parameters, a program to simulate NMR signals, NMR data processing programs, and others. The Kepler software was found to be sufficiently flexible to address several minor implementation challenges without recourse to other software solutions. The automated workflow was demonstrated with data from a [Formula: see text] NMR study of uranyl salts described previously (Cho et al. in J Chem Phys 132:084501, 2010). CONCLUSIONS: The functional implementation of an automated process linking NMR data with electronic structure predictions demonstrates that modern software tools such as Kepler can be used to construct programs that comprehensively manage complex, multi-step scientific workflows spanning several different computers. Automation of the workflow can greatly accelerate the pace of discovery, and allows researchers to focus on the fundamental scientific questions rather than mastery of specialized software and data processing techniques. Future developments that would expand the scope and power of this approach include tools to standardize data and associated metadata formats, and the creation of interactive user interfaces to allow real-time exploration of the effects of program inputs on calculated outputs.

13.
J Phys Chem B ; 120(8): 1601-14, 2016 Mar 03.
Artigo em Inglês | MEDLINE | ID: mdl-26414691

RESUMO

Kinetic energy dependent reactions of Th(+) with H2, D2, and HD were studied using a guided ion beam tandem mass spectrometer. Formation of ThH(+) and ThD(+) is endothermic in all cases with similar thresholds. Branching ratio results for the reaction with HD indicate that Th(+) reacts via a statistical mechanism, similar to Hf(+). The kinetic energy dependent cross sections for formation of ThH(+) and ThD(+) were evaluated to determine a 0 K bond dissociation energy (BDE) of D0(Th(+)-H) = 2.45 ± 0.07 eV. This value is in good agreement with a previous result obtained from analysis of the Th(+) + CH4 reaction. D0(Th(+)-H) is observed to be larger than its transition metal congeners, TiH(+), ZrH(+), and HfH(+), believed to be a result of lanthanide contraction. The reactions with H2 were also explored using quantum chemical calculations that include a semiempirical estimation and explicit calculation of spin-orbit contributions. These calculations agree nicely and indicate that ThH(+) most likely has a (3)Δ1 ground level with a low-lying (1)Σ(+) excited state. Theory also provides the reaction potential energy surfaces and BDEs that are in reasonable agreement with experiment.

14.
J Am Chem Soc ; 137(18): 5911-5, 2015 May 13.
Artigo em Inglês | MEDLINE | ID: mdl-25906363

RESUMO

Activation of the oxo bond of uranyl, UO2(2+), was achieved by collision induced dissociation (CID) of UO2(N3)Cl2(-) in a quadrupole ion trap mass spectrometer. The gas phase complex UO2(N3)Cl2(-) was produced by electrospray ionization of solutions of UO2Cl2 and NaN3. CID of UO2(N3)Cl2(-) resulted in the loss of N2 to form UO(NO)Cl2(-), in which the "inert" uranyl oxo bond has been activated. Formation of UO2Cl2(-) via N3 loss was also observed. Density functional theory computations predict that the UO(NO)Cl2(-) complex has nonplanar Cs symmetry and a singlet ground state. Analysis of the bonding of the UO(NO)Cl2(-) complex shows that the side-on bonded NO moiety can be considered as NO(3-), suggesting a formal oxidation state of U(VI). Activation of the uranyl oxo bond in UO2(N3)Cl2(-) to form UO(NO)Cl2(-) and N2 was computed to be endothermic by 169 kJ/mol, which is energetically more favorable than formation of NUOCl2(-) and UO2Cl2(-). The observation of UO2Cl2(-) during CID is most likely due to the absence of an energy barrier for neutral ligand loss.

15.
Inorg Chem ; 54(7): 3584-99, 2015 Apr 06.
Artigo em Inglês | MEDLINE | ID: mdl-25768128

RESUMO

The reaction of atomic thorium cations with CH4 (CD4) and the collision-induced dissociation (CID) of ThCH4(+) with Xe are studied using guided ion beam tandem mass spectrometry. In the methane reactions at low energies, ThCH2(+) (ThCD2(+)) is the only product; however, the energy dependence of the cross-section is inconsistent with a barrierless exothermic reaction as previously assumed on the basis of ion cyclotron resonance mass spectrometry results. The dominant product at higher energies is ThH(+) (ThD(+)), with ThCH3(+) (ThCD3(+)) having a similar threshold energy. The latter product subsequently decomposes at still higher energies to ThCH(+) (ThCD(+)). CID of ThCH4(+) yields atomic Th(+) as the exclusive product. The cross-sections of all product ions are modeled to provide 0 K bond dissociation energies (in eV) of D0(Th(+)-H) ≥ 2.25 ± 0.18, D0(Th(+)-CH) = 6.19 ± 0.16, D0(Th(+)-CH2) ≥ 4.54 ± 0.09, D0(Th(+)-CH3) = 2.60 ± 0.30, and D0(Th(+)-CH4) = 0.47 ± 0.05. Quantum chemical calculations at several levels of theory are used to explore the potential energy surfaces for activation of methane by Th(+), and the effects of spin-orbit coupling are carefully considered. When spin-orbit coupling is explicitly considered, a barrier for C-H bond activation that is consistent with the threshold measured for ThCH2(+) formation (0.17 ± 0.02 eV) is found at all levels of theory, whereas this barrier is observed only at the BHLYP and CCSD(T) levels otherwise. The observation that the CID of the ThCH4(+) complex produces Th(+) as the only product with a threshold of 0.47 eV indicates that this species has a Th(+)(CH4) structure, which is also consistent with a barrier for C-H bond activation. This barrier is thought to exist as a result of the mixed ((4)F,(2)D) electronic character of the Th(+) J = (3)/2 ground level combined with extensive spin-orbit effects.

16.
J Phys Chem A ; 117(47): 12256-67, 2013 Nov 27.
Artigo em Inglês | MEDLINE | ID: mdl-24168210

RESUMO

Car-Parrinello molecular dynamics (CPMD) simulations have been used to examine the hydration structures, coordination energetics, and the first hydrolysis constants of Pu(3+), Pu(4+), PuO2(+), and PuO2(2+) ions in aqueous solution at 300 K. The coordination numbers and structural properties of the first shell of these ions are in good agreement with available experimental estimates. The hexavalent PuO2(2+) species is coordinated to five aquo ligands while the pentavalent PuO2(+) complex is coordinated to four aquo ligands. The Pu(3+) and Pu(4+) ions are both coordinated to eight water molecules. The first hydrolysis constants obtained for Pu(3+) and PuO2(2+) are 6.65 and 5.70, respectively, all within 0.3 pH unit of the experimental values (6.90 and 5.50, respectively). The hydrolysis constant of Pu(4+), 0.17, disagrees with the value of -0.60 in the most recent update of the Nuclear Energy Agency Thermochemical Database (NEA-TDB) but supports recent experimental findings. The hydrolysis constant of PuO2(+), 9.51, supports the experimental results of Bennett et al. [Radiochim. Acta 1992, 56, 15]. A correlation between the pKa of the first hydrolysis reaction and the effective charge of the plutonium center was found.

17.
Inorg Chem ; 52(19): 11269-79, 2013 Oct 07.
Artigo em Inglês | MEDLINE | ID: mdl-24024761

RESUMO

The structures and bonding of gas-phase [(UO2)2(OH)n](4-n) (n = 2-6) complexes have been studied using density functional theory (DFT), MP2, and CCSD(T) methods with particular emphasis on ground state structures featuring cation-cation interactions (CCIs) between the uranyl groups. An interesting trend is observed in the stabilities of members of this series of complexes. The structures of [(UO2)2(OH)2](2+), [(UO2)2(OH)4], and [(UO2)2(OH)6](2-) featuring CCIs are found at higher energies (by 3-27 kcal/mol) in comparison to their conventional µ2-dihydroxo structures. In contrast, the CCI structures of [(UO2)2(OH)3](+) and [(UO2)2(OH)5](-) are respectively degenerate with and lower in energy than the structures with the µ2-dihydroxo format. The origin of this trend lies in the symmetry-based need to balance the coordination numbers and effective atomic charges of each uranium center. The calculated IR vibrational frequencies provide signature probes that can be used in differentiating the low-energy structures and in experimentally confirming the existence of the structures featuring CCIs.

18.
J Chem Phys ; 139(3): 034301, 2013 Jul 21.
Artigo em Inglês | MEDLINE | ID: mdl-23883021

RESUMO

We present an EOMCCSD (equation of motion coupled cluster with singles and doubles) study of excited states of the small [UO2](2+) and [UO2](+) model systems as well as the larger U(VI)O2(saldien) complex. In addition, the triples contribution within the EOMCCSDT and CR-EOMCCSD(T) (completely renormalized EOMCCSD with non-iterative triples) approaches for the [UO2](2+) and [UO2](+) systems as well as the active-space variant of the CR-EOMCCSD(T) method-CR-EOMCCSd(t)-for the U(VI)O2(saldien) molecule are investigated. The coupled cluster data were employed as benchmark to choose the "best" appropriate exchange-correlation functional for subsequent time-dependent density functional (TD-DFT) studies on the transition energies for closed-shell species. Furthermore, the influence of the saldien ligands on the electronic structure and excitation energies of the [UO2](+) molecule is discussed. The electronic excitations as well as their oscillator dipole strengths modeled with TD-DFT approach using the CAM-B3LYP exchange-correlation functional for the [U(V)O2(saldien)](-) with explicit inclusion of two dimethyl sulfoxide molecules are in good agreement with the experimental data of Takao et al. [Inorg. Chem. 49, 2349 (2010)].

19.
J Phys Chem A ; 117(23): 4988-95, 2013 Jun 13.
Artigo em Inglês | MEDLINE | ID: mdl-23675905

RESUMO

Enthalpies of formation for the ThX4 and UX4 (X = F, Cl, OH) species have been investigated with density functional theory and coupled-cluster methods. ThX4 molecules are all confirmed as tetrahedral, while all UX4 molecules are predicted to adopt D2d symmetry using density functional theory. Multireference coupled cluster approaches confirm the D2d symmetry for UF4. The bonding is mostly ionic, and predicted formation energies for the halogen species show good agreement with experiment. Our calculated hydration energy of UF4 (-54.0 kcal/mol) is in very good agreement with the experimental data (-54.8 kcal/mol). We predict CCSD(T) formation energies of ΔfG[U(OH)4(g)] = -286.3 kcal/mol and ΔfG[U(OH)4(aq)] = -318.7 kcal/mol. ΔfG[U(OH)4(aq)] is 21 kcal/mol less stable than the established experimental thermodynamic data.


Assuntos
Compostos Organometálicos/química , Teoria Quântica , Termodinâmica , Tório/química , Urânio/química
20.
J Cheminform ; 5(1): 25, 2013 May 24.
Artigo em Inglês | MEDLINE | ID: mdl-23705910

RESUMO

BACKGROUND: Multidisciplinary integrated research requires the ability to couple the diverse sets of data obtained from a range of complex experiments and computer simulations. Integrating data requires semantically rich information. In this paper an end-to-end use of semantically rich data in computational chemistry is demonstrated utilizing the Chemical Markup Language (CML) framework. Semantically rich data is generated by the NWChem computational chemistry software with the FoX library and utilized by the Avogadro molecular editor for analysis and visualization. RESULTS: The NWChem computational chemistry software has been modified and coupled to the FoX library to write CML compliant XML data files. The FoX library was expanded to represent the lexical input files and molecular orbitals used by the computational chemistry software. Draft dictionary entries and a format for molecular orbitals within CML CompChem were developed. The Avogadro application was extended to read in CML data, and display molecular geometry and electronic structure in the GUI allowing for an end-to-end solution where Avogadro can create input structures, generate input files, NWChem can run the calculation and Avogadro can then read in and analyse the CML output produced. The developments outlined in this paper will be made available in future releases of NWChem, FoX, and Avogadro. CONCLUSIONS: The production of CML compliant XML files for computational chemistry software such as NWChem can be accomplished relatively easily using the FoX library. The CML data can be read in by a newly developed reader in Avogadro and analysed or visualized in various ways. A community-based effort is needed to further develop the CML CompChem convention and dictionary. This will enable the long-term goal of allowing a researcher to run simple "Google-style" searches of chemistry and physics and have the results of computational calculations returned in a comprehensible form alongside articles from the published literature.

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