Gaussian Basis Set and Planewave Relativistic Spin−Orbit Methods in NWChem

Magnetic Field Effect on the Oxidation of Unsaturated Compounds by Molecular Oxygen

A quantum-chemical analysis of the effect of a constant magnetic field on radical formation in the processes of chain oxidation of organic compounds by molecular oxygen is presented. The calculation of the total electronic energies and thermodynamic functions of the compounds involved in the reactions was performed by the density functional method with the hybrid exchange-correlation functional of Becke, Lee, Yang and Parr DFT B3LYP/6-311G** using the NWChem software package. The effect of the magnetic field on the individual stages of chain oxidation is associated with the evolution of radical pairs. It is assumed that the dipole–dipole interaction in a radical pair is not averaged by the diffusion of radicals and should be taken into account. To a large extent, the magnetic field effect (MFE) value is influenced by the ratio between the relaxation time of the oscillatory-excited state in the radical pair (tvib) and the relaxation time of the inter-combination transitions (tst). Although the developed technique refers to liquid-phase reactions, it can be used to study the MFE for oxidation of biologically significant compounds in multiphase systems, such as micelles, liposomes and membranes.

Resonant Inelastic X-ray Scattering Calculations of Transition Metal Complexes Within a Simplified Time-Dependent Density Functional Theory Framework

We present a time-dependent density functional theory (TDDFT) approach to compute the light-matter couplings between two different manifolds of excited states relative to a common ground state in the context of 4d transition metal systems. These quantities are the necessary ingredients to solve the Kramers-Heisenberg (KH) equation for resonant inelastic X-ray scattering (RIXS) and several other types of two-photon spectroscopies. The procedure is based on the pseudo-wavefunction approach, where the solutions of a TDDFT calculation can be used to construct excited-state wavefunctions, and on the restricted energy window approach, where a manifold of excited states can be rigorously defined based on the energies of the occupied molecular orbitals involved in the excitation process. Thus, the present approach bypasses the need to solve the costly TDDFT quadratic-response equations. We illustrate the applicability of the method to 4d transition metal molecular complexes by calculating the 2p4d RIXS maps of three representative ruthenium complexes and comparing them to experimental results. The method can capture all the experimental features in all three complexes to allow the assignment of the experimental peaks, with relative energies correct to within ∼0.6 eV at the cost of two independent TDDFT calculations.

Revealing the bonding of solvated Ru complexes with valence-to-core resonant inelastic X-ray scattering

Ru-complexes are widely studied because of their use in biological applications and photoconversion technologies. We reveal novel insights into the chemical bonding of a series of Ru(ii)- and Ru(iii)-complexes by leveraging recent advances in high-energy-resolution tender X-ray spectroscopy and theoretical calculations. We perform Ru 2p4d resonant inelastic X-ray scattering (RIXS) to probe the valence excitations in dilute solvated Ru-complexes. Combining these experiments with a newly developed theoretical approach based on time-dependent density functional theory, we assign the spectral features and quantify the metal-ligand bonding interactions. The valence-to-core RIXS features uniquely identify the metal-centered and charge transfer states and allow extracting the ligand-field splitting for all the complexes. The combined experimental and theoretical approach described here is shown to reliably characterize the ground and excited valence states of Ru complexes, and serve as a basis for future investigations of ruthenium, or other 4d metals active sites, in biological and chemical applications.

Simulated field-modulated x-ray absorption in titania

In this paper, we present a method to compute the x-ray absorption near-edge structure (XANES) spectra of solid-state transition metal oxides using real-time time-dependent density functional theory, including spin-orbit coupling effects. This was performed on bulk-mimicking anatase titania (TiO₂) clusters, which allows for the use of hybrid functionals and atom-centered all electron basis sets. Furthermore, this method was employed to calculate the shifts in the XANES spectra of the Ti L-edge in the presence of applied electric fields to understand how external fields can modify the electronic structure, and how this can be probed using x-ray absorption spectroscopy. Specifically, the onset of t_2g peaks in the Ti L-edge was observed to red shift and the e_g peaks were observed to blue shift with increasing fields, attributed to changes in the hybridization of the conduction band (3d) orbitals.

NWChem: Past, present, and future

Specialized computational chemistry packages have permanently reshaped the landscape of chemical and materials science by providing tools to support and guide experimental efforts and for the prediction of atomistic and electronic properties. In this regard, electronic structure packages have played a special role by using first-principle-driven methodologies to model complex chemical and materials processes. Over the past few decades, the rapid development of computing technologies and the tremendous increase in computational power have offered a unique chance to study complex transformations using sophisticated and predictive many-body techniques that describe correlated behavior of electrons in molecular and condensed phase systems at different levels of theory. In enabling these simulations, novel parallel algorithms have been able to take advantage of computational resources to address the polynomial scaling of electronic structure methods. In this paper, we briefly review the NWChem computational chemistry suite, including its history, design principles, parallel tools, current capabilities, outreach, and outlook.

Formation of Cerium and Neodymium Isocyanides in the Reactions of Cyanogen with Ce and Nd Atoms in Argon Matrices

Laser ablation of metallic Ce and Nd reacting with cyanogen in excess argon during codeposition at 4 K forms Ce(NC)_x and Nd(NC)_x for x = 1-3, which are identified from their matrix infrared spectra using cyanogen substituted with ¹³C and ¹⁵N. The electronic structure calculations were performed for isocyano and cyano Cd and Nd compounds for up to n = 4. The frequencies were calculated at the density functional theory level with three different functionals as well as correlated molecular orbital theory (MP2) and are consistent with the experimental assignments and the corresponding ¹²C/¹³C isotopic frequency ratios for the isocyano species. The computed frequencies for the analogous cyanide complexes are significantly higher than those for the isocyano isomers, and they are not observed in the spectra. The high spin isocyano complexes are the lowest energy structures. On the basis of the natural population analysis results, the bonding in ⁴CeNC and ⁶NdNC is essentially purely ionic with the Ce/Nd in the +I-oxidation state. The bonding for disocyano (³Ce(NC)₂ and ⁵Nd(NC)₂) and triisocyano (²Ce(NC)₃ and ⁴Nd(NC)₃) complexes is still quite ionic with the lanthanide in the +II and +III formal oxidation states, respectively. For ¹Ce(NC)₄, the oxidation state is best described as being between +III and +IV. Formation of ⁵Nd(NC)₄ does not really change the electron configuration on the Nd from that in ⁴Nd(NC)₃ and the oxidation state on the Nd remains at +III. Although Nd compounds with up to 3 NC^- groups have more ionic binding than do the corresponding Ce compounds, Ce(NC)₄ has more ionic binding than does Nd(NC)₄. The ionic nature of isocyano Ce and Nd complexes decreases as the number of isocyano groups increases. The energetics of formation of the isocyano Ce and Nd complexes using cyanogen or CN radicals are calculated to be mostly due to exothermic processes, with the exothermicity decreasing as the number of isocyano groups increases.

Potential Energy Surface of Group 11 Trimers (Cu, Ag, Au): Bond Angle Isomerism in Au3

Potential energy surfaces for the group 11 trimers were generated at various levels of coupled-cluster theory to examine the effects of Jahn-Teller distortions. Our calculations show that the lowest-energy conformer for Cu₃, Ag₃, and Au₃ is the ²B₂ (∼65° isomer) without spin-orbit corrections. Spin-orbit corrections have negligible contributions to the relative energies for the angle dependence of the potential energy surfaces for Cu₃ and Ag₃. The inclusion of spin-orbit corrections for Au₃ makes the ²B₂ (∼65°) and ²A₁ (∼55°) states approximately degenerate. A novel ²B₂ isomer of Au₃ at an obtuse angle of ∼125° was also characterized, providing evidence for bond angle isomerism on the same ²B₂ potential energy surface. Spin-orbit corrections increase the barrier height between the ²B₂ (65°) and ²B₂ (125°) bond angle isomers of Au₃. The calculated symmetric stretch vibrational frequencies are in good agreement with the available experimental values. All frequencies calculated for the Au₃ ²B₂ (∼125°) state are real, and there is at least one bound bending vibration for this state. Jahn-Teller parameters are also derived for each trimer.

Heteroleptic Ir(III)N6 Complexes with Long-Lived Triplet Excited States and in Vitro Photobiological Activities

A series of cationic heteroleptic iridium(III) complexes bearing tris-diimine ligands [Ir(phen)2(R-phen)]3+ (R-phen = phenanthroline (1), 3,8-diphenylphenanthroline (2), 3,8-dipyrenylphenanthroline (3), 3-phenylphenanthroline (4), 3-pyrenylphenanthroline (5), and 3,8-diphenylethynylphenanthroline (6)) were synthesized and characterized. These complexes possessed phen ligand-localized 1π,π* transitions below 300 nm, and charge transfer (1CT) and/or 1π,π* transitions between 300 and 520 nm. In 1, 2, 4, and 6, the low-energy bands were mixed 1CT/1π,π*. However, the increased π-donating ability of the pyrenyl substituent(s) in 3 and 5 split the low-energy bands into a pyrene-based 1π,π* transition at 300-380 nm and an intraligand charge transfer (1ILCT) transition at 380-520 nm. All complexes were emissive at room temperature in CH3CN, but the parentage of the emitting state varied depending on the R substituent(s). Complex 1 exhibited predominantly phen ligand-localized 3π,π* emission mixed with metal-to-ligand charge transfer (3MLCT) character, whereas the emission of 2, 4, and 6 was predominantly from the excited-state with 3π,π*/3ILCT/3MLCT character. The emission from 3 and 5 was dominated by pyrene-based 3π,π* states mixed with 3ILCT character. The different natures of the lowest triplet excited states were also reflected by the different spectral features and lifetimes of the triplet transient absorption of these complexes. Complexes 3 and 5 had singlet oxygen quantum yields as high as 81 and 72%, respectively. Both gave submicromolar phototoxicities toward cancer cells (SK-MEL-28 human melanoma) and bacteria ( S. aureus and S. mutans) with visible-light activation (and marginal to no photobiological activity with red light). Their visible-light phototherapeutic indices (PIs) toward SK-MEL-28 cells were 248 for 3 and >435 for 5; PIs were lower in bacteria (≤62) because of their inherent antimicrobial activities. Both complexes were shown to produce substantial amounts of intracellular reactive oxygen species (ROS), which may account for their photobiological activities.

Emerging investigator series: methylmercury speciation and dimethylmercury production in sulfidic solutions

Alkylated mercury species (monomethylmercury, MeHg, and dimethylmercury, DMeHg) exhibit significant bioaccumulation, and pose significant risks to ecosystems and human health. Although decades of research have been devoted to understanding MeHg formation and degradation, little is known about the DMeHg formation in aquatic systems. Here, we combine complementary experimental and computational approaches to examine MeHg speciation and DMeHg formation in sulfidic aqueous solutions, with an emphasis on the formation and decomposition of the binuclear bis(methylmercuric(ii)) sulfide complex (CH3Hg)2S. Experimental data indicate that the reaction 2CH3Hg+ + HS- ⇄ (CH3Hg)2S + H+ has a log K = 26.0 ± 0.2. Thus, the binuclear (CH3Hg)2S complex is likely to be the dominant MeHg species under high MeHg concentrations typically used in experimental investigations of MeHg degradation by sulfate-reducing bacteria (SRB). Our finding of a significant abiotic removal mechanism for MeHg in sulfidic solutions through the formation of relatively insoluble (CH3Hg)2S suggests careful reexamination of reported "oxidative demethylation" of MeHg by SRB and perhaps other obligate anaerobes. We provide evidence for slow decomposition of (CH3Hg)2S to DMeHg and HgS, with a first-order rate constant k = 1.5 ± 0.4 × 10-6 h-1. Quantum chemical calculations suggest that the reaction proceeds by a novel mechanism involving rearrangement of the (CH3Hg)2S complex facilitated by strong Hg-Hg interactions that activate a methyl group for intramolecular transfer. Predictions of DMeHg formation rates under a variety of field and laboratory conditions indicate that this pathway for DMeHg formation will be significant in laboratory experiments utilizing high MeHg concentrations, favoring (CH3Hg)2S formation. In natural systems with relatively high MeHg/[H2S]T ratios (the oxic/anoxic interface, for example), DMeHg production may be observed, and warrants further investigation.

Magnetic Ordering in Gold Nanoclusters

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 Au25(SCH2CH2Ph)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 using electron paramagnetic resonance (EPR). As a film, Au25(SCH2CH2Ph)18 0 exhibits a paramagnetic behavior, but at low temperature, ferromagnetic interactions are detectable. One or few single crystals undergo physical reorientation with the applied field and exhibit 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 (SO) coupling and crystal distortion are important to determine the observed magnetic behaviors. Density functional theory calculations carried out on single cluster and periodic models predict the values of SO coupling and crystal-splitting 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 monodisperse with atomic precision, (ii) of known charge state, and (iii) well-defined in terms of crystallinity and experimental conditions.

Benchmark Study of Density Functional Theory for Neutral Gold Clusters, Aun (n = 2-8)

Neutral gold clusters, Au_n (n = 2-8), were optimized using coupled cluster singles and doubles with perturbative triples (CCSD(T)) with a triple-ζ-level basis set to develop reliable reference values for their structural and energy parameters in order to assess the performance of density functionals. The performance of 44 density functional theory (DFT) methods for calculating molecular structures and relative energies is assessed with respect to CCSD(T). In addition, their performance when calculating vertical ionization potentials (vIPs) of Au_n (n = 2-8) is also assessed by comparison with experimental values. The revTPSS functional shows good performance for calculating both the structural and energy properties of Au_n (n = 2-8), whereas B3P86 shows a remarkable performance in calculating the vIPs. The quadruple-ζ-level valence basis set is necessary for obtaining accurate energy values in CCSD(T) calculations.

Spin-Orbit Effect on the Molecular Properties of TeXn (X = F, Cl, Br, and I; n = 1, 2, and 4): A Density Functional Theory and Ab Initio Study

Density functional theory (DFT) and ab initio calculations, including spin-orbit coupling (SOC), were performed to investigate the spin-orbit (SO) effect on the molecular properties of tellurium halides, TeXn (X = F, Cl, Br, and I; n = 1, 2, and 4). SOC elongates the Te-X bond and slightly reduces the vibrational frequencies. Consideration of SOC leads to better agreement with experimental values. Møller-Plesset second-order perturbation theory (MP2) seriously underestimates the Te-X bond lengths. In contrast, B3LYP significantly overestimates them. SO-PBE0 and multireference configuration interactions with the Davidson correction (MRCI+Q), which include SOC via a state-interaction approach, give the Te-I bond length of TeI2 that matches the experimental value. On the basis of the calculated thermochemical energy and optimized molecular structure, TeI4 is unlikely to be stable. The use of PBE0 including SOC is strongly recommended for predicting the molecular properties of Te-containing compounds.

A theoretical study on the reaction of ozone with aqueous iodide

Atmospheric iodine chemistry plays a key role in tropospheric ozone catalytic destruction, new particle formation, and as one of the possible sinks of gaseous polar elemental mercury. Moreover, it has been recently proposed that reaction of ozone with iodide on the sea surface could be the major contributor to the chemical loss of atmospheric ozone. However, the mechanism of the reaction between aqueous iodide and ozone is not well known. The aim of this paper is to improve the understanding of such a mechanism. In this paper, an ab initio study of the reaction of aqueous iodide and ozone is presented, evaluating thermodynamic data of the different reactions proposed in previous experimental studies. In addition, the structures, energetics and possible evolution of the key IOOO(-) intermediate are discussed for the first time.

Kohn–Sham calculations of NMR shifts for paramagnetic 3d metal complexes: protocols, delocalization error, and the curious amide proton shifts of a high-spin iron(ii) macrocycle complex

Ligand chemical shifts (pNMR shifts) are analyzed using DFT. A large difference in the amide proton shifts of a high-spin Fe(ii) complex arises from O → Fe dative bonding which only transfers β spin density to the metal.

Structures, vibrational frequencies, and stabilities of halogen cluster anions and cations, X(n)(+/-), n = 3, 4, and 5

The structures, vibrational frequencies, and thermodynamic stabilities of the homonuclear polyhalogen ions, X3(+), X3(-), X4(+), X4(-), X5(+), and X5(-) (X = Cl, Br, I), have been calculated at the CCSD(T) level. The energetics were calculated using the Feller-Peterson-Dixon approach for the prediction of reliable enthalpies of formation. The calculations allow the following predictions where stabilities are defined in terms of thermodynamic quantities. (1) The X3(+) cations are stable toward loss of X2; (2) the X3(-) anions are marginally stable toward loss of X2 with Cl3(-) being the least stable; (3) the X4(+) cations and X4(-) anions are only weakly bound dimers of X2(+1/2) and X2(-1/2) units, respectively, but the cations are marginally stable toward decomposition to X3(+) and X, with I4(+) having the lowest dissociation energy, whereas the X4(-) anions decompose spontaneously to X3(-) and X; (4) the X5(+) cations are only marginally stable at low temperatures toward loss of X2, with Cl5(+) being the least stable; and (5) the X5(-) anions are also only stable at low temperatures toward loss of X2, with Cl5(-) being the least stable.

Relativistic calculations of magnetic resonance parameters: background and some recent developments

This article outlines some basic concepts of relativistic quantum chemistry and recent developments of relativistic methods for the calculation of the molecular properties that define the basic parameters of magnetic resonance spectroscopic techniques, i.e. nuclear magnetic resonance shielding, indirect nuclear spin-spin coupling and electric field gradients (nuclear quadrupole coupling), as well as with electron paramagnetic resonance g-factors and electron-nucleus hyperfine coupling. Density functional theory (DFT) has been very successful in molecular property calculations, despite a number of problems related to approximations in the functionals. In particular, for heavy-element systems, the large electron count and the need for a relativistic treatment often render the application of correlated wave function ab initio methods impracticable. Selected applications of DFT in relativistic calculation of magnetic resonance parameters are reviewed.

Molecular structure and stability of dissolved lithium polysulfide species

We present a molecular level study of the dissolution mechanism and subsequent chemical stability of lithium polysulfide species using a combined experimental and theoretical approach.

Simulating Ru L3-edge X-ray absorption spectroscopy with time-dependent density functional theory: model complexes and electron localization in mixed-valence metal dimers

Ruthenium L3-edge X-ray absorption (XA) spectroscopy probes unoccupied 4d orbitals of the metal atom and is increasingly being used to investigate the local electronic structure in ground and excited electronic states of Ru complexes. The simultaneous development of computational tools for simulating Ru L3-edge spectra is crucial for interpreting the spectral features at a molecular level. This study demonstrates that time-dependent density functional theory (TDDFT) is a viable and predictive tool for simulating ruthenium L3-edge XA spectroscopy. We systematically investigate the effects of exchange correlation functional and implicit and explicit solvent interactions on a series of Ru(II) and Ru(III) complexes in their ground and electronic excited states. The TDDFT simulations reproduce all of the experimentally observed features in Ru L3-edge XA spectra within the experimental resolution (0.4 eV). Our simulations identify ligand-specific charge transfer features in complicated Ru L3-edge spectra of [Ru(CN)6](4-) and Ru(II) polypyridyl complexes illustrating the advantage of using TDDFT in complex systems. We conclude that the B3LYP functional most accurately predicts the transition energies of charge transfer features in these systems. We use our TDDFT approach to simulate experimental Ru L3-edge XA spectra of transition metal mixed-valence dimers of the form [(NC)5M(II)-CN-Ru(III)(NH3)5](-) (where M = Fe or Ru) dissolved in water. Our study determines the spectral signatures of electron delocalization in Ru L3-edge XA spectra. We find that the inclusion of explicit solvent molecules is necessary for reproducing the spectral features and the experimentally determined valencies in these mixed-valence complexes. This study validates the use of TDDFT for simulating Ru 2p excitations using popular quantum chemistry codes and providing a powerful interpretive tool for equilibrium and ultrafast Ru L3-edge XA spectroscopy.

Perspective: relativistic effects

This perspective article discusses some broadly-known and some less broadly-known consequences of Einstein's special relativity in quantum chemistry, and provides a brief outline of the theoretical methods currently in use, along with a discussion of recent developments and selected applications. The treatment of the electron correlation problem in relativistic quantum chemistry methods, and expanding the reach of the available relativistic methods to calculate all kinds of energy derivative properties, in particular spectroscopic and magnetic properties, requires on-going efforts.

Linear-Response and Real-Time Time-Dependent Density Functional Theory Studies of Core-Level Near-Edge X-Ray Absorption

We discuss our implementation and application of time-dependent density functional theory (TDDFT) to core-level near-edge absorption spectroscopy, using both linear-response (LR) and real-time (RT) approaches. We briefly describe our restricted excitation window TDDFT (REW-TDDFT) approach for core excitations, which has also been reported by other groups. This is followed by a detailed discussion of real-time TDDFT techniques tailored to core excitations, including obtaining spectral information through delta-function excitation, postprocessing time-dependent signals, and resonant excitation through quasi-monochromatic excitation. We present results for the oxygen K-edge of water and carbon monoxide; the carbon K-edge of carbon monoxide; the ruthenium L3-edge for the hexaamminerutheium(III) ion, including scalar relativistic corrections via the zeroth order regular approximation (ZORA); and the carbon and fluorine K-edges for a series of fluorobenzenes. In all cases, the calculated spectra are found to be in reasonable agreement with experimental results, requiring only a uniform shift ranging from -4 eV to +19 eV, i.e., on the order of a few percent of the excitation energy. Real-time TDDFT visualization of excited state charge densities is used to visually examine the nature of each excitation, which gives insight into the effects of atoms bound to the absorbing center.