Comparison of Computational Strategies for the Calculation of the Electronic Coupling in Intermolecular Energy and Electron Transport Processes.

Electronic couplings in intermolecular electron and energy transfer processes calculated by six different existing computational techniques are compared to nonorthogonal configuration interaction for fragments (NOCI-F) results. The paper addresses the calculation of the electronic coupling in diketopyrrolopyrol, tetracene, 5,5'-difluoroindigo, and benzene-Cl for hole and electron transport, as well as the local exciton and singlet fission coupling. NOCI-F provides a rigorous computational scheme to calculate these couplings, but its computational cost is rather elevated. The here-considered ab initio Frenkel-Davydov (AIFD), Dimer projection (DIPRO), transition dipole moment coupling, Michl-Smith, effective Hamiltonian, and Mulliken-Hush approaches are computationally less demanding, and the comparison with the NOCI-F results shows that the NOCI-F results in the couplings for hole and electron transport are rather accurately predicted by the more approximate schemes but that the NOCI-F exciton transfer and singlet fission couplings are more difficult to reproduce.

Special Topic on High Performance Computing in Chemical Physics.

Computational modeling and simulation have become indispensable scientific tools in virtually all areas of chemical, biomolecular, and materials systems research. Computation can provide unique and detailed atomic level information that is difficult or impossible to obtain through analytical theories and experimental investigations. In addition, recent advances in micro-electronics have resulted in computer architectures with unprecedented computational capabilities, from the largest supercomputers to common desktop computers. Combined with the development of new computational domain science methodologies and novel programming models and techniques, this has resulted in modeling and simulation resources capable of providing results at or better than experimental chemical accuracy and for systems in increasingly realistic chemical environments.

Multilayer Divide-Expand-Consolidate Coupled-Cluster Method: Demonstrative Calculations of the Adsorption Energy of Carbon Dioxide in the Mg-MOF-74 Metal-Organic Framework.

The implementation and evaluation of a multilayer extension of the divide-expand-consolidate (DEC) scheme within the LSDalton program is presented. The DEC scheme is a linear-scaling, fragmentation-based local coupled-cluster (CC) method that provides a means of overcoming the scaling wall associated with canonical CC electronic structure calculations on large molecular systems. Taking advantage of the local nature of correlation effects, the correlation energy for the full molecule is calculated from a set of independent fragments using localized molecular orbitals. However, when only a small subsystem of a larger system is of interest, for example, adsorption sites or catalytically active sites, the majority of the computational time may be spent evaluating the correlation energy of fragments which have little effect on the properties in the area of interest (AOI). The multilayer DEC (ML-DEC) scheme addresses this by taking advantage of the independent nature of the fragments in order to evaluate the correlation energy of various regions of the system at different levels of theory. Regions far from the AOI are evaluated at lower (cheaper) levels of theory such as Hartree-Fock (HF) or Møller-Plesset second-order perturbation theory (MP2), while the area immediately surrounding the AOI is treated with a higher level CC model. Through the ML-DEC scheme, the computational cost of CC calculations on these types of systems can be significantly reduced while maintaining the accuracy of higher-level calculations. Results from HF/RI-MP2 and RI-MP2/CCSD ML-DEC calculations of the binding energy of a fatty acid dimer are presented. We find that the ML-DEC scheme is capable of reproducing DEC energy differences at a target level of theory, provided that the region treated at the target level of theory is chosen to be sufficiently large. Time-to-solution is found to be significantly reduced, particularly in the RI-MP2/CCSD calculations. Finally, the ML-DEC scheme is applied to the calculation of CO2 adsorption in a Mg-MOF-74 channel.

Molecular and Dissociative Adsorption of Water on (TiO2)n Clusters, n = 1-4.

The low energy structures of the (TiO2)n(H2O)m (n ≤ 4, m ≤ 2n) and (TiO2)8(H2O)m (m = 3, 7, 8) clusters were predicted using a global geometry optimization approach, with a number of new lowest energy isomers being found. Water can molecularly or dissociatively adsorb on pure and hydrated TiO2 clusters. Dissociative adsorption is the dominant reaction for the first two H2O adsorption reactions for n = 1, 2, and 4, for the first three H2O adsorption reactions for n = 3, and for the first four H2O adsorption reactions for n = 8. As more H2O's are added to the hydrated (TiO2)n cluster, dissociative adsorption becomes less exothermic as all the Ti centers become 4-coordinate. Two types of bonds can be formed between the molecularly adsorbed water and TiO2 clusters: a Lewis acid-base Ti-O(H2) bond or an O···H hydrogen bond. The coupled cluster CCSD(T) results show that at 0 K the H2O adsorption energy at a 4-coordinate Ti center is ∼15 kcal/mol for the Lewis acid-base molecular adsorption and ∼7 kcal/mol for the H-bond molecular adsorption, in comparison to that of 8-10 kcal/mol for the dissociative adsorption. The cluster size and geometry independent dehydration reaction energy, ED, for the general reaction 2(-TiOH) → -TiOTi- + H2O at 4-coordinate Ti centers was estimated from the aggregation reaction of nTi(OH)4 to form the monocyclic ring cluster (TiO3H2)n + nH2O. ED is estimated to be -8 kcal/mol, showing that intramolecular and intermolecular dehydration reactions are intrinsically thermodynamically allowed for the hydrated (TiO2)n clusters with all of the Ti centers 4-coordinate, which can be hindered by cluster geometry changes caused by such processes. Bending force constants for the TiOTi and OTiO bonds are determined to be 7.4 and 56.0 kcal/(mol·rad(2)). Infrared vibrational spectra were calculated using density functional theory, and the new bands appearing upon water adsorption were assigned.

Non-orthogonal Configuration Interaction Study on the Effect of Thermal Distortions on the Singlet Fission Process in Photoexcited Pure and B,N-Doped Pentacene Crystals.

The present computational work analyzes singlet fission (SF) as a pathway for multiplication of photogenerated excitons in crystalline polyacenes. Our study explores the well-known crystalline pentacene (C22H14) and the prospective and potentially interesting doped B,N-pentacene (BC20NH14). At the molecular level, the singlet fission process involves a pair of neighboring molecules and is based on the coupling between an excited singlet state (S1S0) and two singlet-coupled triplets (1T1T1), which, typically, is influenced by an intermolecular charge transfer state. Taking data from periodic density functional theory and ab initio wave function calculations, we applied the non-orthogonal configuration interaction method to determine electronic coupling parameters. The comparison of the results for both equilibrium structures reveal smaller SF coupling for pentacene than for B,N-pentacene by a factor of ∼5. Introduction of the dynamic behavior to the crystals (vibrations, thermal motion) provides a more realistic picture of the effect of the disorder at the molecular level on the SF efficiency. The coupling values associated to out-of-equilibrium structures show that most of the S1S0/1T1T1 couplings remain virtually constant or slightly increase for pentacene when molecular disorder is introduced. Homologous calculations on B,N-pentacene show a generalized decrease in the coupling values, notably if large phonon displacements are considered. A few of the structures analyzed feature much larger SF coupling if some distortion results in (nearly) degenerate charge transfer and excited singlet and triplet states. For these particular situations, an acceleration of the SF process could occur although in competition with electron-hole separation as an alternative pathway.

Differential tapasin dependence of MHC class I molecules correlates with conformational changes upon peptide dissociation: a molecular dynamics simulation study.

Efficiency of peptide loading to MHC class I molecules in the endoplasmic reticulum is allele specific and can involve interaction with tapasin and other proteins. Allele HLA-B 4,402 depends on tapasin whereas HLA-B 4,405 (Tyr116 instead of Asp in B 4,402) can efficiently load peptides without tapasin. Both alleles adopt very similar structures in the presence of the same peptide. Molecular dynamics simulations on peptide termini dissociation from the alpha(1)/alpha(2) binding domains were used to characterize structural and free energy changes. The magnitude of the calculated free energy change and the shape of the free energy curve vs. distance for induced peptide C terminus dissociation differed for B 4,405 compared to B 4,402. Structural changes during C terminus dissociation occurred mainly in the first segment of the alpha(2)-helix that flanks the peptide C terminus binding region (F pocket) and contacts residue 116. This segment is also close to the proposed tapasin contact region. For B 4402, a stable shift towards an altered open F pocket structure deviating significantly from the bound form was observed. In contrast, B 4405 showed only a transient opening of the F pocket followed by relaxation towards a structure close to the bound (receptive) form upon C terminus dissociation. The greater tendency for a peptide-receptive conformation in the absence of peptide combined with more long-range interactions with the peptide C terminus facilitates peptide binding to B 4405 and correlates with the tapasin-independence of this allele. A possible role of tapasin in case of HLA-B 4402 and other tapasin-dependent alleles could be the stabilization of a peptide-receptive class I conformation.

Engineering an ultra-stable affinity reagent based on Top7.

Antibodies are widely used for diagnostic and therapeutic applications because of their sensitive and specific recognition of a wide range of targets; however, their application is limited by their structural complexity. More demanding applications require greater stability than can be achieved by immunoglobulin-based reagents. Highly stable, protein-based affinity reagents are being investigated for this role with the goal of identifying a suitable scaffold that can attain specificity and sensitivity similar to that of antibodies while performing under conditions where antibodies fail. We have engineered Top7--a highly stable, computationally designed protein--to specifically bind human CD4 by inserting a peptide sequence derived from a CD4-specific antibody. Molecular dynamics simulations were used to evaluate the structural effect of the peptide insertion at a specific site within Top7 and suggest that this Top7 variant retains conformational stability over 100 degrees C. This engineered protein specifically binds CD4 and, consistent with simulations, is extremely resistant to thermal and chemical denaturation--retaining its secondary structure up to at least 95 degrees C and requiring 6 M guanidine to completely unfold. This CD4-specific protein demonstrates the functionality of Top7 as a viable scaffold for use as a general affinity reagent which could serve as a robust and inexpensive alternative to antibodies.

In vitro evolution of a peptide with a hematite binding motif that may constitute a natural metal-oxide binding archetype.

Phage-display technology was used to evolve peptides that selectively bind to the metal-oxide hematite (Fe2O3) from a library of approximately 3 billion different polypeptides. The sequences of these peptides contained the highly conserved amino acid motif, Ser/Thr-hydrophobic/aromatic-Ser/Thr-Pro-Ser/Thr. To better understand the nature of the peptide-metal oxide binding demonstrated by these experiments, molecular dynamics simulations were carried out for Ser-Pro-Ser at a hematite surface. These simulations show that hydrogen bonding occurs between the two serine amino acids and the hydroxylated hematite surface and that the presence of proline between the hydroxide residues restricts the peptide flexibility, thereby inducing a structural-binding motif. A search of published sequence data revealed that the binding motif (Ser/Thr-Pro-Ser/Thr) is adjacent to the terminal heme-binding domain of both OmcA and MtrC, which are outer membrane cytochromes from the metal-reducing bacterium Shewanella oneidensis MR-1. The entire five amino acid consensus sequence (Ser/Thr-hydrophobic/ aromatic-Ser/Thr-Pro-Ser/Thr) was also found as multiple copies in the primary sequences of metal-oxide binding proteins Sil1 and Sil2 from Thalassiosira pseudonana. We suggest that this motif constitutes a natural metal-oxide binding archetype that could be exploited in enzyme-based biofuel cell design and approaches to synthesize tailored metal-oxide nanostructures.