Coupled-cluster with active space selected higher amplitudes: performance of seminatural orbitals for ground and excited state calculations

The active space approach for coupled-cluster models is generalized using the general active space concept and implemented in a string-based general coupled-cluster code. Particular attention is devoted to the choice of orbitals on which the subspace division is based. Seminatural orbitals are proposed for that purpose. These orbitals are obtained by diagonalizing only the hole-hole and particle-particle block of the one-electron density of a lower-order method. The seminatural orbitals are shown to be a good replacement for complete active space self-consistent field orbitals and avoid the ambiguities with respect to the reference determinant introduced by the latter orbitals. The seminatural orbitals also perform well in excited state calculations, including excited states with strong double excitation contributions, which usually are difficult to describe with standard coupled-cluster methods. A set of vertical excitation energies is obtained and benchmarked against full configuration interaction calculations, and alternative hierarchies of active space coupled-cluster models are proposed. As a simple application the spectroscopic constants of the C(2) B (1)Delta(g) and B(') (1)Sigma(g) (+) states are calculated using active space coupled-cluster methods and basis sets up to quadruple-zeta quality in connection with extrapolation and additivity schemes.     

Constant-time through-bond 13C correlation spectroscopy for assigning protein resonances with solid-state NMR spectroscopy

Even as available magnetic fields for NMR continue to increase, resolution remains one of the most critical limitations in assigning and solving structures of larger biomolecules. Here we present a novel constant-time through-bond correlation spectroscopy for solids that offers superior resolution for 13C chemical shift assignments in proteins. In this experiment, the indirect evolution and transfer periods are combined into a single constant time interval, offering increased resolution while not sacrificing sensitivity. In GB1, this allows us to resolve peaks that are otherwise unresolved and to make assignments in the absence of multibond transfers.     

Analysis of current research addressing complementary use of life-cycle assessment and risk assessment for engineered nanomaterials: have lessons been learned from previous experience with chemicals?

While it is generally agreed that successful strategies to address the health and environmental impacts of engineered nanomaterials (NM) should consider the well-established frameworks for conducting life-cycle assessment (LCA) and risk assessment (RA), scientific research, and specific guidance on how to practically apply these methods are still very much under development. This paper evaluates how research efforts have applied LCA and RA together for NM, particularly reflecting on previous experiences with applying these methods to chemicals. Through a literature review and a separate analysis of research focused on applying LCA and RA together for NM, it appears that current research efforts have taken into account some key ??lessons learned?? from previous experience with chemicals while many key challenges remain for practically applying these methods to NM. We identified two main approaches for using these methods together for NM: ??LC-based RA?? (traditional RA applied in a life-cycle perspective) and ??RA-complemented LCA?? (conventional LCA supplemented by RA in specific life-cycle steps). Hence, the latter is the only identified approach which genuinely combines LC- and RA-based methods for NM-risk research efforts to date as the former is rather a continuation of normal RA according to standard assessment procedures (e.g., REACH). Both these approaches along with recommendations for using LCA and RA together for NM are similar to those made previously for chemicals, and thus, there does not appear to be much progress made specific for NM. We have identified one issue in particular that may be specific for NM when applying LCA and RA at this time: the need to establish proper dose metrics within both methods.     

The Impact of Retinal Configuration on the Protein–Chromophore Interactions in Bistable Jumping Spider Rhodopsin-1

Bistable rhodopsins have two stable forms that can be interconverted by light. Due to their ability to act as photoswitches, these proteins are considered as ideal candidates for applications such as optogenetics. In this work, we analyze a recently crystalized bistable rhodopsin, namely the jumping spider rhodopsin-1 (JSR1). This rhodopsin exhibits identical absorption maxima for the parent and the photoproduct form, which impedes its broad application. We performed hybrid QM/MM simulations to study three isomers of the retinal chromophore: the 9-cis, 11-cis and all-trans configurations. The main aim was to gain insight into the specific interactions of each isomer and their impact on the absorption maximum in JSR1. The absorption spectra were computed using sampled snapshots from QM/MM molecular dynamics trajectories and compared to their experimental counterparts. The chromophore–protein interactions were analyzed by visualizing the electrostatic potential of the protein and projecting it onto the chromophore. It was found that the distance between a nearby tyrosine (Y126) residue plays a larger role in the predicted absorption maximum than the primary counterion (E194). Geometric differences between the isomers were also noted, including a structural change in the polyene chain of the chromophore, as well as changes in the nearby hydrogen bonding network.     

Spin–orbit and correlation effects in platinum hydride (PtH)

The low-lying electronic states of PtH were studied by all-electron one- and two-component variational calculations on the multireference CI levels. The orbital optimization is performed within a one-component formalism, whereas the further refinement of the wave functions follows two different schemes: The most demanding approach introduces spin–orbit coupling in the CI optimization step, giving a simultaneous treatment of electron correlation and spin–orbit coupling. The second, considerably less demanding approach, corresponds almost to a perturbational treatment, introducing spin–orbit coupling as a final step after the CI optimization by diagonalizing the resulting Hamiltonian matrix over CI states. © 1998 John Wiley & Sons, Inc. Int J Quant Chem 68: 53–64, 1998     

Phage Langmuir monolayers and Langmuir–Blodgett films

Stable, insoluble Langmuir monolayer films composed of Staphylococcus aureus-specific lytic bacteriophage were formed at an air–water interface and characterized. The phage monolayer was very strong, withstanding a surface pressure of ～40 mN/m at 20 °C. The surface pressure–area (Π–A) isotherm possessed a shoulder at ～7 × 10⁴ nm²/phage particle, attributed to a change in phage orientation at the air–water interface from horizontal to vertical capsid-down/tail-up orientation as surface pressure was increased. The Π–A-dependence was accurately described using the Volmer equation of state, assuming horizontal orientation to an air–water interface at low surface pressures with an excluded area per phage particle of 4.6 × 10⁴ nm². At high pressures phage particles followed the space-filling densely packed disks model with a specific area of 8.5 × 10³ nm²/phage particle. Lytic phage monolayers were transferred onto gold-coated silica substrates from the air–water interface at a constant surface pressure of 18 mN/m by Langmuir–Blodgett method, then dried and analyzed by scanning electron microscopy (SEM) and ellipsometry. Phage specific adsorption (Γ) in Langmuir–Blodgett (LB) films measured by SEM was consistent with that calculated independently from Π–A isotherms at the transfer surface pressure of 18 mN/m (Γ = 23 phage particles/μm²). The 50 nm-thickness of phage monolayer measured by ellipsometer agreed well with the horizontal phage average size estimated by SEM. Surface properties of phage Langmuir monolayer compare well with other monolayers formed from nano- and micro-particles at the air–water interface and similar to that of classic amphiphiles 1,2-diphytanoyl-sn-glycero-3-phosphocholine (phospholipid) and stearic acid.