Reversible Photochromism of 4,4'-Disubstituted 2,2'-Bipyridine in the Presence of SO3.

We report an unusual photochromic behavior of 4,4'-disubstituted-2,2'-bipyridine. It was found that in the presence of a SO3 source and HCl, 2,2'-bipyridine-4,4'-dibutyl ester undergoes a color change from yellow to magenta in solution with maximum absorbance at 545 nm upon irradiation with 395 nm light. The photochromism is thermally reversible in solution. Different from the known bipyridine-based photoswitching pathways, the photo response does not involve any metal which form colored complexes or the formation of colored free radical cations like the photo-reduction of viologens. A combination of experimental and computational analysis was used to probe the mechanism. The results suggest the colored species to be a complex formed between N-oxide of the 2,2'-bipyridine-4,4'-dibutyl ester and SO2; the N-oxide and SO2 are formed from photoactivated oxidation of the bipyridine with SO3 serving as the oxygen source. This complex represents a new addition to the library of photoswitches that is easy to synthesize, reversible in solution, and of high fatigue resistance, making it a promising candidate for applications in photo-switchable materials and SO3 detection. We also demonstrated experimentally similar photochromic behaviors with 2,2'-bipyridine-containing polymers.

Novel Triangulenes: Computational Investigations of Energy Thresholds for Photocatalytic Water Splitting.

Organic materials with Inverted Singlet-Triplet (INVEST) gaps are interesting for their potential use in photocatalytic small molecule transformations such as the entirely solar-driven water splitting reaction. However, only a few INVEST emitters are thermodynamically able to split water requiring a first singlet excited dark state, S1 , above 1.27 or 1.76 eV, and absorption near solar the maximum, 2.57 eV. These requirements and the INVEST character are key for achieving a long-lived photocatalyst for water splitting. The only known INVEST emitters that conform to these criteria are large triangular boron carbon nitrides with unknown synthesis pathways. Using ADC(2), a quantum-mechanical method, we describe three triangulenes. 3 a is a cyano azacyclopenta[cd]phenalene derivative while 3 b and 3 c are cycl[3.3.3]azine derivatives. 3 b has a previously undescribed disulfide bridge. Overall, 3 a fulfills requirements for photocatalytic four-electron reduction of water while the S1 states of 3 b and 3 c are likely slightly low for the two-electron reduction process. By analyzing impacts of ligands, we find that there are guidelines describing how S1 -S5 energies and oscillator strengths, T1 energies, and ΔES1T1 gaps are affected, requiring deep-learning algorithms for which studies will be presented by us in due time. The impact of ground-state geometries, solvation effects, as well as reduced-cost ADC(2) algorithms on our findings are also discussed.

Building on the strengths of a double-hybrid density functional for excitation energies and inverted singlet-triplet energy gaps.

It is demonstrated that a double hybrid density functional approximation, ωB88PTPSS, that incorporates equipartition of density functional theory and the non-local correlation, however with a meta-generalized gradient approximation correlation functional, as well as with the range-separated exchange of ωB2PLYP, provides accurate excitation energies for conventional systems, as well as correct prescription of negative singlet-triplet gaps for non-conventional systems with inverted gaps, without any necessity for parametric scaling of the same-spin and opposite-spin non-local correlation energies. Examined over "safe" excitations of the QUESTDB set, ωB88PTPSS performs quite well for open-shell systems, correctly and fairly accurately [relative to equation-of-motion coupled-cluster singles and doubles (EOM-CCSD) reference] predicts negative gaps for 50 systems with inverted singlet-triplet gaps, and is one of the leading performers for intramolecular charge-transfer excitations and achieves near-second-order approximate coupled cluster (CC2) and second-order algebraic diagrammatic construction quality for the Q1 and Q2 subsets. Subsequently, we tested ωB88PTPSS on two sets of real-life examples from recent computational chemistry literature-the low energy bands of chlorophyll a (Chl a) and a set of thermally activated delayed fluorescence (TADF) systems. For Chl a, ωB88PTPSS qualitatively and quantitatively achieves DLPNO-STEOM-CCSD-level performance and provides excellent agreement with experiment. For TADF systems, ωB88PTPSS agrees quite well with spin-component-scaled CC2 (SCS-CC2) excitation energies, as well as experimental values, for the gaps between the S1 and T1 excited states.

Improving the Brightness of Pyronin Fluorophore Systems through Quantum-Mechanical Predictions.

The pyronin class of fluorophores serves a critical role in numerous imaging applications, particularly involving preferential staining of RNA through base pair intercalation. Despite this important role in molecular staining applications, the same set of century-old pyronins (i.e., pyronin Y (PY) and pyronin B (PB)), which possess relatively low fluorophore brightness, are still predominantly being used due to the lack of methodology for generating enhanced variants. Here, we use TD-DFT calculations of interconversion energies between structures on the S1 surface as a preliminary means to evaluate fluorophore brightness for a proposed set of pyronins containing variable substitution patterns at the 2, 3, 6, and 7 positions. Using a nucleophilic aromatic substitution/hydride addition approach, we synthesized the same set of pyronins and demonstrate that quantum-mechanical computations are useful for predicting fluorophore performance. We produced the brightest series of pyronin fluorophores described to date, which possess considerable gains over PY and PB.

DFT Analysis of Methane C-H Activation and Over-Oxidation by [Cu2 O]2+ and [Cu2 O2 ]2+ Sites in Zeolite Mordenite: Intra- versus Inter-site Over-Oxidation.

Methane over-oxidation by copper-exchanged zeolites prevents realization of high-yield catalytic conversion. However, there has been little description of the mechanism for methane over-oxidation at the copper active sites of these zeolites. Using density functional theory (DFT) computations, we reported that tricopper [Cu3 O3 ]2+ active sites can over-oxidize methane. However, the role of [Cu3 O3 ]2+ sites in methane-to-methanol conversion remains under debate. Here, we examine methane over-oxidation by dicopper [Cu2 O]2+ and [Cu2 O2 ]2+ sites using DFT in zeolite mordenite (MOR). For [Cu2 O2 ]2+ , we considered the µ-(η2 :η2 ) peroxo-, and bis(µ-oxo) motifs. These sites were considered in the eight-membered (8MR) ring of MOR. µ-(η2 :η2 ) peroxo sites are unstable relative to the bis(µ-oxo) motif with a small interconversion barrier. Unlike [Cu2 O]2+ which is active for methane C-H activation, [Cu2 O2 ]2+ has a very large methane C-H activation barrier in the 8MR. Stabilization of methanol and methyl at unreacted dicopper sites however leads to over-oxidation via sequential hydrogen atom abstraction steps. For methanol, these are initiated by abstraction of the CH3 group, followed by OH and can proceed near 200 °C. Thus, for [Cu2 O]2+ and [Cu2 O2 ]2+ species, over-oxidation is an inter-site process. We discuss the implications of these findings for methanol selectivity, especially in comparison to the intra-site process for [Cu3 O3 ]2+ sites and the role of Brønsted acid sites.

Copper-Oxo Active Sites for Methane C-H Activation in Zeolites: Molecular Understanding of Impact of Methane Hydroxylation on UV-Vis Spectra.

Here, we analyze changes in the optical spectra of activated copper-exchanged zeolites during methane activation with the Tamm-Dancoff time-dependent density functional theory, TDA-DFT, while using the ωB2PLYP functional. Two active sites, [Cu2O]2+ and [Cu3O3]2+, were studied. For [Cu2O]+, the 22 700 cm-1 peak is associated with µ-oxo 2p → Cu 3d/4s charge transfer. Of the [Cu2O]2+ methane C-H activation intermediates that we examined, only [Cu-O(H)(H)-Cu] and [Cu-O(H)(CH3)-Cu] have spectra that match experimental observations. After methane activation, the µ-oxo 2p orbitals lose two electrons and become hybridized with methanol C 2p orbitals and/or H 1s orbitals. The frontier unoccupied orbitals become more Cu 4s/4p Rydberg-like, reducing overlap with occupied orbitals. These effects cause the disappearance of the 22 700 cm-1 peak. For [Cu3O3]2+, the exact structures of the species formed after methane activation are unknown. Thus, we considered eight possible structures. Several of these provide a significant decrease in intensity near 23 000-38 000 cm-1, as seen experimentally. Notably, these species involve either rebound of the separated methyl to a µ-oxo atom or its remote stabilization at a Brønsted acid site in exchange for the acidic proton. These spectral changes are caused by the same mechanism seen in [Cu2O]2+ and are likely responsible for the observed reduced intensities near 23 000-38 000 cm-1. Thus, TDA-DFT calculations with ωB2PLYP provide a molecular-level understanding of the evolution of copper-oxo active sites during methane-to-methanol conversion.

Methane C-H Activation by [Cu2O]2+ and [Cu3O3]2+ in Copper-Exchanged Zeolites: Computational Analysis of Redox Chemistry and X-ray Absorption Spectroscopy.

There is an ongoing debate regarding the role of [Cu3O3]2+ in methane-to-methanol conversion by copper-exchanged zeolites. Here, we perform electronic structure analysis and localized orbital bonding analysis to probe the redox chemistry of its Cu and µ-oxo sites. Also, the X-ray absorption near-edge structure, XANES, of methane activation in [Cu3O3]2+ is compared to that of the more ubiquitous [Cu2O]2+. Methane C-H activation is associated with only the Cu2+/Cu+ redox couple in [Cu2O]2+. For [Cu3O3]2+, there is no basis for the Cu3+/Cu2+ couple's participation at the density functional theory ground state. In [Cu3O3]2+, there are many possible intrazeolite intermediates for methane activation. In the nine possibilities that we examined, methane activation is driven by a combination of the Cu2+/Cu+ and oxyl/O2- redox couples. Based on this, the Cu 1s-edge XANES spectra of [Cu2O]2+ and [Cu3O3]2+ should both have energy signatures of Cu2+ → Cu+ reduction during methane activation. This is indeed what we obtained from the calculated XANES spectra. [Cu2O]2+ and [Cu3O3]2+ intermediates with one Cu+ site are shifted by 0.9-1.7 eV, while those with two Cu+ sites are shifted by 3.0-4.2 eV. These are near a range of 2.5-3.2 eV observed experimentally after contacting methane with activated copper-exchanged zeolites. Thus, activation of methane by [Cu3O3]2+ will lead to formation of Cu+ sites. Importantly, for future quantitative XANES studies, involvement of O- + e- → O2- in [Cu3O3]2+ implies a disconnect between the overall reactivity and the number of electrons used in the Cu2+/Cu+ redox couple.

Methane Over-Oxidation by Extra-Framework Copper-Oxo Active Sites of Copper-Exchanged Zeolites: Crucial Role of Traps for the Separated Methyl Group.

Copper-exchanged zeolites are useful for stepwise conversion of methane to methanol at moderate temperatures. This process also generates some over-oxidation products like CO and CO2 . However, mechanistic pathways for methane over-oxidation by copper-oxo active sites in these zeolites have not been previously described. Adequate understanding of methane over-oxidation is useful for developing systems with higher methanol yields and selectivities. Here, we use density functional theory (DFT) to examine methane over-oxidation by [Cu3 O3 ]2+ active sites in zeolite mordenite MOR. The methyl group formed after activation of a methane C-H bond can be stabilized at a µ-oxo atom of the active site. This µ-(O-CH3 ) intermediate can undergo sequential hydrogen atom abstractions till eventual formation of a copper-monocarbonyl species. Adsorbed formaldehyde, water and formates are also formed during this process. The overall mechanistic path is exothermic, and all intermediate steps are facile at 200 °C. Release of CO from the copper-monocarbonyl costs only 3.4 kcal/mol. Thus, for high methanol selectivities, the methyl group from the first hydrogen atom abstraction step must be stabilized away from copper-oxo active sites. Indeed, it must be quickly trapped at an unreactive site (short diffusion lengths) while avoiding copper-oxo species (large paths between active sites). This stabilization of the methyl group away from the active sites is central to the high methanol selectivities obtained with stepwise methane-to-methanol conversion.

Time-Dependent Density Functional Theory Study of Copper(II) Oxo Active Sites for Methane-to-Methanol Conversion in Zeolites.

Copper-exchanged zeolites are useful materials for step-wise methane-to-methanol conversion (MMC). However, methanol yields on copper-exchanged zeolites are often modest, spurring interest in the development of active-site species that are activated at moderate temperatures, afford greater yields, and provide excellent methanol selectivities. Ultraviolet-visible (UV-vis) spectroscopy is a major tool for characterizing the active-sites and their evolution during the step-wise MMC process. However, computation of the UV-vis spectra of the copper-oxo active sites using Tamm-Dancoff time-dependent density functional theory (TDA-DFT) can be quite problematic. This has led to utilization of expensive methods based on multireference approaches, Green functions, and the Bethe-Salpeter equation. In this work, we examined the optical spectra of [CuO]+, [Cu2O]2+, [Cu2O2]2+, and [Cu3O3]2+ species implicated in MMC in zeolites. For the larger species, we examined how agreement with experimental data is improved with increasingly larger cluster models. For [CuO]+, we compared TDA-DFT against restricted active space 2nd-order perturbation theory, RASPT2. We found that signature peaks for [CuO]+ have multireference behavior. The excited states have many configuration state functions with a double excitation character. These effects are likely responsible for the poor utility of conventional TDA-DFT methods. Indeed, we obtain good agreement with experimental data and RASPT2 after accounting for 2h/2p excitations within TDA-DFT with a previously described configuration interaction singles and doubles, CIS(D)-style scheme. This was the case for [CuO]+, [Cu2O]2+, as well as a [Cu2O2]2+ species. Using a long-range corrected double-hybrid, ωB2PLYP, we provide for the first time computational evidence for the experimental UV-vis spectrum of the [Cu3O3]2+ active site motif.

2D-IR studies of cyanamides (NCN) as spectroscopic reporters of dynamics in biomolecules: Uncovering the origin of mysterious peaks.

Cyanamides (NCN) have been shown to have a larger transition dipole strength than cyano-probes. In addition, they have similar structural characteristics and vibrational lifetimes to the azido-group, suggesting their utility as infrared (IR) spectroscopic reporters for structural dynamics in biomolecules. To access the efficacy of NCN as an IR probe to capture the changes in the local environment, several model systems were evaluated via 2D IR spectroscopy. Previous work by Cho [G. Lee, D. Kossowska, J. Lim, S. Kim, H. Han, K. Kwak, and M. Cho, J. Phys. Chem. B 122(14), 4035-4044 (2018)] showed that phenylalanine analogues containing NCN show strong anharmonic coupling that can complicate the interpretation of structural dynamics. However, when NCN is embedded in 5-membered ring scaffolds, as in N-cyanomaleimide and N-cyanosuccinimide, a unique band structure is observed in the 2D IR spectrum that is not predicted by simple anharmonic frequency calculations. Further investigation indicated that electron delocalization plays a role in the origins of the band structure. In particular, the origin of the lower frequency transitions is likely a result of direct interaction with the solvent.

Activating Water and Hydrogen by Ligand-Modified Uranium and Neptunium Complexes: A Density Functional Theory Study.

Organometallic uranium complexes that can activate small molecules are well-known. In contrast, there are no known organometallic trans-uranium species capable of small-molecule transformations. Using density functional theory, we previously showed that changing actinide-ligand bonds from U-O groups to Np-N- (amide/imido) bonds makes redox small-molecule activation more energetically favorable for Np species. Here, we determine how general this ligand-modulation strategy is for affecting small-molecule activation in Np species. We focus on two reactions, one involving redox transformation of the actinide(s) and the other involving no change in the oxidation state of the actinide(s). Specifically, we considered the hydrogen evolution reaction (HER) from H2O by actinide tris-aryloxide species. We also considered H2 capture and hydride transfer by actinide siloxide and silylamide complexes. For the HER, the barriers for Np(III) systems are much higher than those of U(III). The overall reaction energies are also much worse. An-O → An-N substitutions marginally improve the barriers by 1-4 kcal/mol and more substantially improve the reaction energies by 9-15 kcal/mol. For H2 capture and hydride transfer, the reaction energies for the U and Np species are similar. For both actinides, like-for-like An-O → An-N substitutions lead to improved reaction energies. Interestingly, in a recent report, it seemingly appears that U-O (siloxide) → U-N (silylamide) leads to complete shutdown of reactivity for H2 capture and hydride transfer. This observation is reproduced and explained with calculations. The ligand environments of the siloxide and silylamide that were compared are vastly different. The steric environment of the siloxide is conducive for reactivity while the particular silylamide is not. We conclude that small-molecule activation with organometallic neptunium species is achievable with a guided choice of ligands. Additional emphasis should be placed on ligands that can allow for improved transition state barriers.

Ground-state actinide chemistry with scalar-relativistic multiconfiguration pair-density functional theory.

We have examined the performance of Multiconfiguration Pair-Density Functional Theory (MC-PDFT) for computing the ground-state properties of actinide species. Specifically, we focused on the properties of UN2 and various actinyl species. The properties obtained with MC-PDFT at the scalar-relativistic level are compared to Kohn-Sham DFT (KS-DFT); complete active space self-consistent field theory, CASSCF; coupled-cluster theory, CCSD(T) and CCSDT; as well as multireference perturbation theory (CASPT2). We examine the degree to which MC-PDFT improves over KS-DFT and CASSCF while aligning with CASPT2, CCSD(T), and CCSDT. All properties that we considered were for the CASPT2 electronic ground states. For structural parameters, MC-PDFT confers very little advantage over KS-DFT, especially the B3LYP density functional. For NpO2 3+, MC-PDFT and local KS-DFT functionals excessively favor the bent structure, whereas CCSDT and CASPT2 predict the bent and linear structures as isoenergetic. For this special case, hybrid KS-DFT functionals like PBE0 and B3LYP provide results closer to CASPT2 and CCSDT than MC-PDFT. On a more positive note, MC-PDFT is very close to CASPT2 and CCSD(T) for the redox potentials, energetics of redox chemical reactions, as well as ligand-binding energies. These are encouraging results since MC-PDFT is more affordable. The best MC-PDFT functional is ft-PBE. Our findings suggest that MC-PDFT can be used to study systems and excited states with larger strong electron correlation effects than were considered here. However, for the systems and properties considered here, KS-DFT functionals do well, justifying their usage as the bulwark of computational actinyl chemistry over the last two to three decades.

Pyrazole, Imidazole, and Isoindolone Dipyrrinone Analogues: pH-Dependent Fluorophores That Red-Shift Emission Frequencies in a Basic Solution.

Dipyrrinones are nonfluorescent yellow-pigmented constituents of bilirubin that undergo Z to E isomerization when excited with UV/blue light. Mechanical restriction of the E/Z isomerization process results in highly fluorescent compounds such as N,N-methylene-bridged dipyrrinones and xanthoglows. This manuscript describes the first examples of dipyrrinone analogues, which exhibit fluorescence without covalently linking the pyrole-pyrrolidine nitrogen atoms. Instead these analogues restrict E/Z isomerization through intramolecular hydrogen bonding, resulting in mild to moderately fluorescent compounds (ΦF = 0.01-0.30). Further, in basic solutions (pH > 12), the dipyrrinone analogues readily deprotonate and absorption/emission profiles of the fluorophores red-shifts by 10-49 nm. Directly from commercial materials, 10 analogues were prepared in 41-96% yields in one step. To estimate the capacity of which intramolecular hydrogen bonding has upon restricting the E/Z isomerization process, conformational energies of all analogues, in both the protonated and deprotonated species, were explored by using quantum-mechanical density functional theory (DFT) and time-dependent DFT calculations. The computed strengths of the intramolecular hydrogen bonds are related to the barriers of rotation about the 5-6 bond and both correlate with the experimentally measured fluorescence quantum yields.

Nitrogen Reduction by Multimetallic trans-Uranium Actinide Complexes: A Theoretical Comparison of Np and Pu to U.

There is recent interest in organometallic complexes of the trans-uranium elements. However, preparation and characterization of such complexes are hampered by radioactivity and chemotoxicity issues as well as the air-sensitive and poorly understood behavior of existing compounds. As such, there are no examples of small-molecule activation via redox reactivity of organometallic trans-uranium complexes. This contrasts with the situation for uranium. Indeed, a multimetallic uranium(III) nitride complex was recently synthesized, characterized, and shown to be able to capture and functionalize molecular nitrogen (N2) through a four-electron reduction process, N2 → N24-. The bis-uranium nitride, U-N-U core of this complex is held in a potassium siloxide framework. Importantly, the N24- product could be further functionalized to yield ammonia (NH3) and other desirable species. Using the U-N-U potassium siloxide complex, K3U-N-U, and its cesium analogue, Cs3U-N-U, as starting points, we use scalar-relativistic and spin-orbit coupled density functional theory calculations to shed light on the energetics and mechanism for N2 capture and functionalization. The N2 → N24- reactivity depends on the redox potentials of the U(III) centers and crucially on the stability of the starting complex with respect to decomposition into the mixed oxidation U(IV)/U(III) K2U-N-U or Cs2U-N-U species. For the trans-uranium, Np and Pu analogues of K3U-N-U, the N2 → N24- process is endoergic and would not occur. Interestingly, modification of the Np-O and Pu-O bonds between the actinide cores and the coordinated siloxide framework to Np-NH, Pu-NH, Np-CH2, and Pu-CH2 bonds drastically improves the reaction free energies. The Np-NH species are stable and can reductively capture and reduce N2 to N24-. This is supported by analysis of the spin densities, molecular structure, long-range dispersion effects, as well as spin-orbit coupling effects. These findings chart a path for achieving small-molecule activation with organometallic neptunium analogues of existing uranium complexes.

Performance of density functional theory for describing hetero-metallic active-site motifs for methane-to-methanol conversion in metal-exchanged zeolites.

Methane-to-methanol conversion (MMC) can be facilitated with high methanol selectivities by copper-exchanged zeolites. There are however two open questions regarding the use of these zeolites to facilitate the MMC process. The first concerns the possibility of operating the three cycles in the stepwise MMC process by these zeolites in an isothermal fashion. The second concerns the possibility of improving the methanol yields by systematic substitution of some copper centers in these active sites with other earth-abundant transition metals. Quantum-mechanical computations can be used to compare methane activation by copper oxide species and analogous mixed-metal systems. To carry out such screening, it is important that we use theoretical methods that are accurate and computationally affordable for describing the properties of the hetero-metallic catalytic species. We have examined the performance of 47 exchange-correlation density functionals for predicting the relative spin-state energies and chemical reactivities of six hetero-metallic [M-O-Cu]2+ and [M-O2 -Cu]2+ , (where MCo, Fe, and Ni), species by comparison with coupled cluster theory including iterative single, double excitations as well as perturbative treatment of triple excitations, CCSD(T). We also performed multireference calculations on some of these systems. We considered two types of reactions (hydrogen addition and oxygen addition) that are relevant to MMC. We recommend the use of τ-HCTH and OLYP to determine the spin-state energy splittings in the hetero-metallic motifs. ωB97, ωB97X, ωB97X-D3, and MN15 performed best for predicting the energies of the hydrogen and oxygen addition reactions. In contrast, local, and semilocal functionals do poorly for chemical reactivity. Using [Fe-O-Cu]2+ as a test, we see that the nonlocal functionals perform well for the methane CH activation barrier. In contrast, the semilocal functionals perform rather poorly. © 2018 Wiley Periodicals, Inc.

Predicting Bond Dissociation Energies of Transition-Metal Compounds by Multiconfiguration Pair-Density Functional Theory and Second-Order Perturbation Theory Based on Correlated Participating Orbitals and Separated Pairs.

We study the performance of multiconfiguration pair-density functional theory (MC-PDFT) and multireference perturbation theory for the computation of the bond dissociation energies in 12 transition-metal-containing diatomic molecules and three small transition-metal-containing polyatomic molecules and in two transition-metal dimers. The first step is a multiconfiguration self-consistent-field calculation, for which two choices must be made: (i) the active space and (ii) its partition into subspaces, if the generalized active space formulation is used. In the present work, the active space is chosen systematically by using three correlated-participating-orbitals (CPO) schemes, and the partition is chosen by using the separated-pair (SP) approximation. Our calculations show that MC-PDFT generally has similar accuracy to CASPT2, and the active-space dependence of MC-PDFT is not very great for transition-metal-ligand bond dissociation energies. We also find that the SP approximation works very well, and in particular SP with the fully translated BLYP functional SP-ftBLYP is more accurate than CASPT2. SP greatly reduces the number of configuration state functions relative to CASSCF. For the cases of FeO and NiO with extended-CPO active space, for which complete active space calculations are unaffordable, SP calculations are not only affordable but also of satisfactory accuracy. All of the MC-PDFT results are significantly better than the corresponding results with broken-symmetry spin-unrestricted Kohn-Sham density functional theory. Finally we test a perturbation theory method based on the SP reference and find that it performs slightly worse than CASPT2 calculations, and for most cases of the nominal-CPO active space, the approximate SP perturbation theory calculations are less accurate than the much less expensive SP-PDFT calculations.

What Is the Preferred Conformation of Phosphatidylserine-Copper(II) Complexes? A Combined Theoretical and Experimental Investigation.

Phosphatidylserine (PS) has previously been found to bind Cu2+ in a ratio of 1 Cu2+ ion per 2 PS lipids to form a complex with an apparent dissociation constant that can be as low as picomolar. While the affinity of Cu2+ for lipid membranes containing PS lipids has been well characterized, the structural details of the Cu-PS2 complex have not yet been reported. Coordinating to one amine and one carboxylate moiety on two separate PS lipids, the Cu-PS2 complex is unique among ion-lipid complexes in its ability to adopt both cis and trans conformations. Herein, we determine which stereoisomer of the Cu-PS2 complex is favored in lipid bilayers using density functional theory calculations and electron paramagnetic resonance experiments. It was determined that a conformation in which the nitrogen centers are cis to each other is the preferred binding geometry. This is in contrast to the complex formed when two glycine molecules bind to Cu2+ in bulk solution, where the cis and trans isomers exist in equilibrium, indicating that the lipid environment has a significant steric effect on the Cu2+ binding conformation. These findings are relevant for understanding lipid oxidation caused by Cu2+ binding to lipid membrane surfaces and will help us understand how ion binding to lipid membranes can affect their physical properties.

Structure and Reactivity of X-ray Amorphous Uranyl Peroxide, U2O7.

Recent accidents resulting in worker injury and radioactive contamination occurred due to pressurization of uranium yellowcake drums produced in the western U.S.A. The drums contained an X-ray amorphous reactive form of uranium oxide that may have contributed to the pressurization. Heating hydrated uranyl peroxides produced during in situ mining can produce an amorphous compound, as shown by X-ray powder diffraction of material from impacted drums. Subsequently, studtite, [(UO2)(O2)(H2O)2](H2O)2, was heated in the laboratory. Its thermal decomposition produced a hygroscopic anhydrous uranyl peroxide that reacts with water to release O2 gas and form metaschoepite, a uranyl-oxide hydrate. Quantum chemical calculations indicate that the most stable U2O7 conformer consists of two bent (UO2)(2+) uranyl ions bridged by a peroxide group bidentate and parallel to each uranyl ion, and a µ2-O atom, resulting in charge neutrality. A pair distribution function from neutron total scattering supports this structural model, as do (1)H- and (17)O-nuclear magnetic resonance spectra. The reactivity of U2O7 in water and with water in air is higher than that of other uranium oxides, and this can be both hazardous and potentially advantageous in the nuclear fuel cycle.

Charge Transport in 4 nm Molecular Wires with Interrupted Conjugation: Combined Experimental and Computational Evidence for Thermally Assisted Polaron Tunneling.

We report the synthesis, transport measurements, and electronic structure of conjugation-broken oligophenyleneimine (CB-OPI 6) molecular wires with lengths of ∼4 nm. The wires were grown from Au surfaces using stepwise aryl imine condensation reactions between 1,4-diaminobenzene and terephthalaldehyde (1,4-benzenedicarbaldehyde). Saturated spacers (conjugation breakers) were introduced into the molecular backbone by replacing the aromatic diamine with trans-1,4-diaminocyclohexane at specific steps during the growth processes. FT-IR and ellipsometry were used to follow the imination reactions on Au surfaces. Surface coverages (∼4 molecules/nm(2)) and electronic structures of the wires were determined by cyclic voltammetry and UV-vis spectroscopy, respectively. The current-voltage (I-V) characteristics of the wires were acquired using conducting probe atomic force microscopy (CP-AFM) in which an Au-coated AFM probe was brought into contact with the wires to form metal-molecule-metal junctions with contact areas of ∼50 nm(2). The low bias resistance increased with the number of saturated spacers, but was not sensitive to the position of the spacer within the wire. Temperature dependent measurements of resistance were consistent with a localized charge (polaron) hopping mechanism in all of the wires. Activation energies were in the range of 0.18-0.26 eV (4.2-6.0 kcal/mol) with the highest belonging to the fully conjugated OPI 6 wire and the lowest to the CB3,5-OPI 6 wire (the wire with two saturated spacers). For the two other wires with a single conjugation breaker, CB3-OPI 6 and CB5-OPI 6, activation energies of 0.20 eV (4.6 kcal/mol) and 0.21 eV (4.8 kcal/mol) were found, respectively. Computational studies using density functional theory confirmed the polaronic nature of charge carriers but predicted that the semiclassical activation energy of hopping should be higher for CB-OPI molecular wires than for the OPI 6 wire. To reconcile the experimental and computational results, we propose that the transport mechanism is thermally assisted polaron tunneling in the case of CB-OPI wires, which is consistent with their increased resistance.

Separated-pair approximation and separated-pair pair-density functional theory.

Multi-configuration pair-density functional theory (MC-PDFT) has proved to be a powerful way to combine the capabilities of multi-configuration self-consistent-field theory to represent the an electronic wave function with a highly efficient way to include dynamic correlation energy by density functional theory. All applications reported previously involved complete active space self-consistent-field (CASSCF) theory for the reference wave function. For treating large systems efficiently, it is necessary to ask whether good accuracy is retained when using less complete configuration interaction spaces. To answer this question, we present here calculations employing MC-PDFT with the separated pair (SP) approximation, which is a special case (defined in this article) of generalized active space self-consistent-field (GASSCF) theory in which no more than two orbitals are included in any GAS subspace and in which inter-subspace excitations are excluded. This special case of MC-PDFT will be called SP-PDFT. In SP-PDFT, the electronic kinetic energy and the classical Coulomb energy, the electronic density and its gradient, and the on-top pair density and its gradient are obtained from an SP approximation wave function; the electronic energy is then calculated from the first two of these quantities and an on-top density functional of the last four. The accuracy of the SP-PDFT method for predicting the structural properties and bond dissociation energies of twelve diatomic molecules and two triatomic molecules is compared to the SP approximation itself and to CASSCF, MC-PDFT based on CASSCF, CASSCF followed by second order perturbation theory (CASPT2), and Kohn-Sham density functional theory with the PBE exchange-correlation potential. We show that SP-PDFT reproduces the accuracy of MC-PDFT based on the corresponding CASSCF wave function for predicting C-H bond dissociation energies, the reaction barriers of pericyclic reactions and the properties of open-shell singlet systems, all at only a small fraction of the computational cost.