Software for the frontiers of quantum chemistry: An overview of developments in the Q-Chem 5 package.

This article summarizes technical advances contained in the fifth major release of the Q-Chem quantum chemistry program package, covering developments since 2015. A comprehensive library of exchange-correlation functionals, along with a suite of correlated many-body methods, continues to be a hallmark of the Q-Chem software. The many-body methods include novel variants of both coupled-cluster and configuration-interaction approaches along with methods based on the algebraic diagrammatic construction and variational reduced density-matrix methods. Methods highlighted in Q-Chem 5 include a suite of tools for modeling core-level spectroscopy, methods for describing metastable resonances, methods for computing vibronic spectra, the nuclear-electronic orbital method, and several different energy decomposition analysis techniques. High-performance capabilities including multithreaded parallelism and support for calculations on graphics processing units are described. Q-Chem boasts a community of well over 100 active academic developers, and the continuing evolution of the software is supported by an "open teamware" model and an increasingly modular design.

vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria.

Taxonomic classification of archaeal and bacterial viruses is challenging, yet also fundamental for developing a predictive understanding of microbial ecosystems. Recent identification of hundreds of thousands of new viral genomes and genome fragments, whose hosts remain unknown, requires a paradigm shift away from traditional classification approaches and towards the use of genomes for taxonomy. Here we revisited the use of genomes and their protein content as a means for developing a viral taxonomy for bacterial and archaeal viruses. A network-based analytic was evaluated and benchmarked against authority-accepted taxonomic assignments and found to be largely concordant. Exceptions were manually examined and found to represent areas of viral genome 'sequence space' that are under-sampled or prone to excessive genetic exchange. While both cases are poorly resolved by genome-based taxonomic approaches, the former will improve as viral sequence space is better sampled and the latter are uncommon. Finally, given the largely robust taxonomic capabilities of this approach, we sought to enable researchers to easily and systematically classify new viruses. Thus, we established a tool, vConTACT, as an app at iVirus, where it operates as a fast, highly scalable, user-friendly app within the free and powerful CyVerse cyberinfrastructure.

The Hydrated Electron at the Surface of Neat Liquid Water Appears To Be Indistinguishable from the Bulk Species.

Experiments have suggested that the aqueous electron, e(-)(aq), may play a significant role in the radiation chemistry of DNA. A recent measurement of the energy (below vacuum level) of the putative "interfacial" hydrated electron at the water/vacuum interface, performed using liquid microjet photoelectron spectroscopy, has been interpreted to suggest that aqueous electrons at the water/biomolecule interface may possess the appropriate energetics to induce DNA strand breaks, whereas e(-)(aq) in bulk water lies too far below the vacuum level to induce such reactions. Other such experiments, however, find no evidence of a long-lived feature at low binding energy. We employ a variety of computational strategies to demonstrate that the energetics of the hydrated electron at the surface of neat liquid water are not significantly different from those of e(-)(aq) in bulk water and as such are incompatible with dissociative electron attachment reactions in DNA. We furthermore suggest that no stable interfacial species may exist at all, consistent with the interpretation of certain surface-sensitive spectroscopy measurements, and that even if a short-lived, metastable species does exist at the vacuum/water interface, it would be extremely difficult to distinguish, experimentally, from e(-)(aq) in bulk water, using either optical absorption or photoelectron spectroscopy.

Reparameterization of an Accurate, Few-Parameter Implicit Solvation Model for Quantum Chemistry: Composite Method for Implicit Representation of Solvent, CMIRS v. 1.1.

CMIRS (composite method for implicit representation of solvent) is a relatively new implicit solvation model that adds terms representing solute-solvent dispersion, Pauli repulsion, and hydrogen bonding to a continuum treatment of electrostatics. A small error in the original implementation of the dispersion term, but one that can modify dispersion energies by up to 8 kcal/mol in some cases, necessitates refitting the parameters in the model, which we do here. We refer to the modified implementation and parameter set as CMIRS v. 1.1. While the dispersion energies change in nontrivial ways, an increase in the attractive dispersion term in the new implementation is largely offset by an increase in the Pauli repulsion during the fitting process, such that overall statistical errors are virtually unchanged with respect to v. 1.0 of the model, for a large database of experimental solvation free energies for molecules and ions. Overall, we obtain mean unsigned errors of <0.7 kcal/mol when the solvent is cyclohexane or benzene, <1.5 kcal/mol for water, and <2.8 kcal/mol for dimethyl sulfoxide and acetonitrile, despite using no more than five empirical parameters per solvent. For the important but difficult case of ionic solutes in water, mean unsigned errors are <2.9 kcal/mol.

Comparison of the Marcus and Pekar partitions in the context of non-equilibrium, polarizable-continuum solvation models.

The Marcus and Pekar partitions are common, alternative models to describe the non-equilibrium dielectric polarization response that accompanies instantaneous perturbation of a solute embedded in a dielectric continuum. Examples of such a perturbation include vertical electronic excitation and vertical ionization of a solution-phase molecule. Here, we provide a general derivation of the accompanying polarization response, for a quantum-mechanical solute described within the framework of a polarizable continuum model (PCM) of electrostatic solvation. Although the non-equilibrium free energy is formally equivalent within the two partitions, albeit partitioned differently into "fast" versus "slow" polarization contributions, discretization of the PCM integral equations fails to preserve certain symmetries contained in these equations (except in the case of the conductor-like models or when the solute cavity is spherical), leading to alternative, non-equivalent matrix equations. Unlike the total equilibrium solvation energy, however, which can differ dramatically between different formulations, we demonstrate that the equivalence of the Marcus and Pekar partitions for the non-equilibrium solvation correction is preserved to high accuracy. Differences in vertical excitation and ionization energies are <0.2 eV (and often <0.01 eV), even for systems specifically selected to afford a large polarization response. Numerical results therefore support the interchangeability of the Marcus and Pekar partitions, but also caution against relying too much on the fast PCM charges for interpretive value, as these charges differ greatly between the two partitions, especially in polar solvents.

Empirical Studies on the Network of Social Groups: The Case of Tencent QQ.

BACKGROUND: Participation in social groups are important but the collective behaviors of human as a group are difficult to analyze due to the difficulties to quantify ordinary social relation, group membership, and to collect a comprehensive dataset. Such difficulties can be circumvented by analyzing online social networks. METHODOLOGY/PRINCIPAL FINDINGS: In this paper, we analyze a comprehensive dataset released from Tencent QQ, an instant messenger with the highest market share in China. Specifically, we analyze three derivative networks involving groups and their members-the hypergraph of groups, the network of groups and the user network-to reveal social interactions at microscopic and mesoscopic level. CONCLUSIONS/SIGNIFICANCE: Our results uncover interesting behaviors on the growth of user groups, the interactions between groups, and their relationship with member age and gender. These findings lead to insights which are difficult to obtain in social networks based on personal contacts.

A Structural Model for a Self-Assembled Nanotube Provides Insight into Its Exciton Dynamics.

The design and synthesis of functional self-assembled nanostructures is frequently an empirical process fraught with critical knowledge gaps about atomic-level structure in these noncovalent systems. Here, we report a structural model for a semiconductor nanotube formed via the self-assembly of naphthalenediimide-lysine (NDI-Lys) building blocks determined using experimental 13C-13C and 13C-15N distance restraints from solid-state nuclear magnetic resonance supplemented by electron microscopy and X-ray powder diffraction data. The structural model reveals a two-dimensional-crystal-like architecture of stacked monolayer rings each containing ∼50 NDI-Lys molecules, with significant π-stacking interactions occurring both within the confines of the ring and along the long axis of the tube. Excited-state delocalization and energy transfer are simulated for the nanotube based on time-dependent density functional theory and an incoherent hopping model. Remarkably, these calculations reveal efficient energy migration from the excitonic bright state, which is in agreement with the rapid energy transfer within NDI-Lys nanotubes observed previously using fluorescence spectroscopy.

Calculating Electron-Transfer Coupling with Density Functional Theory: The Long-Range-Corrected Density Functionals.

The density functional theory (DFT) with commonly used functionals is known to be incorrect for charge-transfer problems. With long-range-corrected (LC) density functionals, the asymptotic exchange potential is gradually switched to the Hartree-Fock exchange at a long range, and the prediction for charge-transfer states is greatly improved. In this work, we test LC-DFT's performance on charge-transfer couplings. The range-separation parameter can be tuned nonempirically for properties of a generalized DFT. We propose to minimize the difference of highest-occupied Kohn-Sham orbital energy and the ionization potential (for hole transfer) or the lowest-unoccupied orbital energy and the electron affinity (for electron transfer). For photoinduced charge transfer, the minimum in the sum of such differences for the donor and the acceptor is proposed. With the range-separation parameters optimized, we found that ET couplings derived from the LC-DFT are close to those derived from coupled cluster with singles and doubles. When compared with experimentally derived Mulliken-Hush couplings, LC-DFT couplings are greatly improved as well. We also found that the couplings from BNL and LC-BLYP functionals are generally better than those from LC-ωPBE and LC-ωPBE0. LC-DFT is suitable for calculating ET coupling, especially with this nonempirical approach for the range-separation parameter.

Experimental benchmark data and systematic evaluation of two a posteriori, polarizable-continuum corrections for vertical excitation energies in solution.

We report the implementation and evaluation of a perturbative, density-based correction scheme for vertical excitation energies calculated in the framework of a polarizable continuum model (PCM). Because the proposed first-order correction terms depend solely on the zeroth-order excited-state density, a transfer of the approach to any configuration interaction-type excited-state method is straightforward. Employing the algebraic-diagrammatic construction (ADC) scheme of up to third order as well as time-dependent density-functional theory (TD-DFT), we demonstrate and evaluate the approach. For this purpose, we assembled a set of experimental benchmark data for solvatochromism in molecules (xBDSM) containing 44 gas-phase to solvent shifts for 17 molecules. These data are compared to solvent shifts calculated at the ADC(1), ADC(2), ADC(3/2), and TD-DFT/LRC-ωPBE levels of theory in combination with state-specific as well as linear-response type PCM-based correction schemes. Some unexpected trends and differences between TD-DFT, the levels of ADC, and variants of the PCM are observed and discussed. The most accurate combinations reproduce experimental solvent shifts resulting from the bulk electrostatic interaction with maximum errors in the order of 50 meV and a mean absolute deviation of 20-30 meV for the xBDSM set.

Ab Initio Implementation of the Frenkel-Davydov Exciton Model: A Naturally Parallelizable Approach to Computing Collective Excitations in Crystals and Aggregates.

A fragment-based method for computing vertical excitation energies of molecular clusters is introduced based on an ab initio implementation of a Frenkel-Davydov exciton model consisting of singly excited monomer basis states. Our strategy is to construct and diagonalize the exact Hartree-Fock Hamiltonian in such a basis. Matrix elements between nonorthogonal determinants are computed via the corresponding orbital transformation and the resulting generalized eigenvalue problem is solved to determine collective excitation energies and wave functions. The basis may be expanded to include higher-lying fragment excited states in order to account for interfragment polarization effects. Absolute errors of ≲0.1 eV (relative to supersystem methods) are achievable for systems such as water clusters and crystalline arrays of organic chromophores such as pentacene and napthalenediimide. Preliminary tests for a nine-chromophore subunit of an organic nanotube suggest that it is possible to target the optically bright state, even when it is a high-lying excitation, by using carefully selected basis states. The highly parallel nature of this method provides a foundation for further developments to treat collective excitations in large molecular assemblies.

[Clinical effect of hyperbaric oxygen therapy on groupment acute carbon monoxide poisoning].

OBJECTIVE: To summarize the clinical experience of hyperbaric oxygen therapy in the patients with groupment acute carbon monoxide poisoning. METHOD: 172 patients with acute carbon monoxide poisoning were received hyperbaric oxygen therapy besides some other regular therapies from january 2007 to december 2011. The clinical effect were analyzed retrospectively. RESULTS: 160 patients were cured (93%), 12 cases improved (7%), the total effective rate was 100%. The cure rate of the patients with hyperbaric oxygen therapy within 6 hours after the poisoning for 100% (115/115), It was significantly higher than that of patients treated for more than 6 hours [The cure rate was 78.9% (45/57)], The difference was statistically significant (P < 0.05). CONCLUSION: Treated by hyperbaric oxygen therapy early enough in the patients with acute carbon monoxide poisoning, can prevent or reduce the occurrence of delayed encephalopathy, decreasing disability and mortality.

The role of CH-π interaction in the charge transfer properties in tris(8-hydroxyquinolinato)aluminium(III).

The charge mobility is a key property in many electro-optical materials, with charge transfer (CT) taking place in a solid matrix of molecules. Large intermolecular electronic interaction is one of the key factors for a good CT rate, which is dependent on both intra- and intermolecular structures. The connection of the molecular structure with the intermolecular CT property would facilitate the search for a new material with desirable CT property, but currently it is still quite limited by the lack of knowledge for intermolecular configurations. In the present work, we study factors influencing the intermolecular configurations, and subsequently the CT property, in tris(8-hydroxyquinolinato) aluminium(III) (AlQ(3)) from all currently available crystal structures. We found that there exists a pair of CH-π interactions in a good majority of the π-π stacked bimolecular configurations. Such CH-π and π-π interacting structures are also seen in the crystal structures of many other similar molecules. With both experimental and simulated structures, we show that the CH-π interaction stabilizes the bimolecular configurations, and drives the structure towards a region with a higher electron transfer coupling and lower hole transfer coupling. This effect likely affects the electron transport property of AlQ(3), since it is consistent with recent experimental results, where AlQ(3) analogs with their CH-π interaction blocked either require a higher operating voltage in light-emitting devices [Sapochak et al., J. Am. Chem. Soc., 2001, 123, 6300], or become bipolar in their charge mobilities [Liao et al., J. Am. Chem. Soc., 2009, 131, 763]. CH-π interaction is commonly seen in aromatic molecules, which are frequently used as building blocks in molecules for electro-optical applications. Our work points out a possible way to enhance the desired CT property in the design of new materials.

Ab inito study on triplet excitation energy transfer in photosynthetic light-harvesting complexes.

We have studied the triplet energy transfer (TET) for photosynthetic light-harvesting complexes, the bacterial light-harvesting complex II (LH2) of Rhodospirillum molischianum and Rhodopseudomonas acidophila, and the peridinin-chlorophyll a protein (PCP) from Amphidinium carterae. The electronic coupling factor was calculated with the recently developed fragment spin difference scheme (You and Hsu, J. Chem. Phys. 2010, 133, 074105), which is a general computational scheme that yields the overall coupling under the Hamiltonian employed. The TET rates were estimated based on the couplings obtained. For all light-harvesting complexes studied, there exist nanosecond triplet energy transfer from the chlorophylls to the carotenoids. This result supports a direct triplet quenching mechanism for the photoprotection function of carotenoids. The TET rates are similar for a broad range of carotenoid triplet state energy, which implies a general and robust TET quenching role for carotenoids in photosynthesis. This result is also consistent with the weak dependence of TET kinetics on the type or the number of π conjugation lengths in the carotenoids and their analogues reported in the literature. We have also explored the possibility of forming triplet excitons in these complexes. In B850 of LH2 or the peridinin cluster in PCP, it is unlikely to have triplet exciton since the energy differences of any two neighboring molecules are likely to be much larger than their TET couplings. Our results provide theoretical limits to the possible photophysics in the light-harvesting complexes.

The fragment spin difference scheme for triplet-triplet energy transfer coupling.

To calculate the electronic couplings in both inter- and intramolecular triplet energy transfer (TET), we have developed the "fragment spin difference" (FSD) scheme. The FSD was a generalization from the "fragment charge difference" (FCD) method of Voityuk et al. [J. Chem. Phys. 117, 5607 (2002)] for electron transfer (ET) coupling. In FSD, the spin population difference was used in place of the charge difference in FCD. FSD is derived from the eigenstate energies and populations, and therefore the FSD couplings contain all contributions in the Hamiltonian as well as the potential overlap effect. In the present work, two series of molecules, all-trans-polyene oligomers and polycyclic aromatic hydrocarbons, were tested for intermolecular TET study. The TET coupling results are largely similar to those from the previously developed direct coupling scheme, with FSD being easier and more flexible in use. On the other hand, the Dexter's exchange integral value, a quantity that is often used as an approximate for the TET coupling, varies in a large range as compared to the corresponding TET coupling. To test the FSD for intramolecular TET, we have calculated the TET couplings between zinc(II)-porphyrin and free-base porphyrin separated by different numbers of p-phenyleneethynylene bridge units. Our estimated rate constants are consistent with experimentally measured TET rates. The FSD method can be used for both intermolecular and intramolecular TET, regardless of their symmetry. This general applicability is an improvement over most existing methodologies.

The mediated excitation energy transfer: Effects of bridge polarizability.

The observation of bridge-mediated excitation energy transfer (EET) has raised questions on the physical origin of such an effect. In this work, we studied the effect of bridge fragments in the Coulomb coupling, the major contribution to the electronic coupling in an EET process. For a series of ortho-phenyleneethynylene oligomers spaced donor-acceptors, we found that a large influence of the bridge fragment in EET coupling is through changes in the Coulomb couplings. Both enhancement and screening effects of the bridge were observed as the EET rates were modified by a factor of 0.3-23 with an intervening bridge in our calculations. The dependency of EET couplings on the orientation of transition dipoles of the donor and acceptor from quantum mechanical computations is very similar to that of a simple classical dielectric model. Our work shows that the bridge fragments can modify the Coulomb coupling with their polarizability by providing an optical dielectric medium between the donor and acceptor. In particular, when the transition dipoles of the donor and acceptor were longitudinal to a polarizable bridge, the EET rates were enhanced by one order of magnitude, as compared to the values of through-space models. Our results offer important insights into the design of efficient energy transfer systems.

Triplet-triplet energy-transfer coupling: theory and calculation.

Triplet-triplet (TT) energy transfer requires two molecular fragments to exchange electrons that carry different spin and energy. In this paper, we analyze and report values of the electronic coupling strengths for TT energy transfer. Two different methods were proposed and tested: (1) Directly calculating the off-diagonal Hamiltonian matrix element. This direct coupling scheme was generalized from the one used for electron transfer coupling, where two spin-localized unrestricted Hartree-Fock wave functions are used as the zero-order reactant and product states, and the off-diagonal Hamiltonian matrix elements are calculated directly. (2) From energy gaps derived from configuration-interaction-singles (CIS) scheme. Both methods yielded very similar results for the systems tested. For TT coupling between a pair of face-to-face ethylene molecules, the exponential attenuation factor is 2.59 A(-1)(CIS6-311+G(**)), which is about twice as large as typical values for electron transfer. With a series of fully stacked polyene pairs, we found that the TT coupling magnitudes and attenuation rates are very similar irrespective of their molecular size. If the polyenes were partially stacked, TT couplings were much reduced, and they decay more rapidly with distance than those of full-stacked systems. Our results showed that the TT coupling arises mainly from the region of close contact between the donor and acceptor frontier orbitals, and the exponential decay of the coupling with separation depends on the details of the molecular contacts. With our calculated results, nanosecond or picosecond time scales for TT energy-transfer rates are possible.

Charge transport properties of tris(8-hydroxyquinolinato)aluminum(III): why it is an electron transporter.

The charge transport properties of mer-tris(8-hydroxyquinolinato)aluminum(III) (mer-Alq), which is the most widely used electron transport material in OLED, were investigated by quantum chemistry calculations within the framework of the charge hopping model and Marcus electron transfer theory. Internal reorganization energies of 0.276 and 0.242 eV were calculated by the DFT-B3LYP method employing a 6-31 G* basis set for the electrons lambdai(e) and holes lambdai(h), respectively. The relative distances and orientations of Alq molecules in amorphous film were simulated by those in the beta-phase. The intermolecular charge-transfer integrals, Hda(h) and Hda(e), along all 14 hopping pathways were then calculated by the Koopmans Theorem in conjunction with the Hartree-Fock method employing a 6-31 G* basis set as well as by the direct coupling method. The results showed that there were some Hda(e) that were 1 order of magnitude larger than any Hda(h), because hopping pathways with effective overlaps of LUMOs can occur and, thus, large Hda(e). On the other hand, effective overlap of HOMO was absent in all pathways, resulting in a relatively small Hda(h). This difference in the magnitudes of Hda(e) and Hda(h) would predict a 2 orders of magnitude difference in the electron-transfer rate constants and account for the observed 2 orders of magnitude difference in the mobilities of electrons and holes.