Compressed intramolecular dispersion interactions.

The feasibility of the compression of localized virtual orbitals is explored in the context of intramolecular long-range dispersion interactions. Singular value decomposition (SVD) of coupled cluster doubles amplitudes associated with the dispersion interactions is analyzed for a number of long-chain systems, including saturated and unsaturated hydrocarbons and a silane chain. Further decomposition of the most important amplitudes obtained from these SVDs allows for the analysis of the dispersion-specific virtual orbitals that are naturally localized. Consistent with previous work on intermolecular dispersion interactions in dimers, it is found that three important geminals arise and account for the majority of dispersion interactions at the long range, even in the many body intramolecular case. Furthermore, it is shown that as few as three localized virtual orbitals per occupied orbital can be enough to capture all pairwise long-range dispersion interactions within a molecule

Generalized Unitary Coupled Cluster Wavefunctions for Quantum Computation

We introduce a unitary coupled-cluster (UCC) ansatz termed $k$-UpCCGSD that is based on a family of sparse generalized doubles (D) operators which provides an affordable and systematically improvable unitary coupled-cluster wavefunction suitable for implementation on a near-term quantum computer. $k$-UpCCGSD employs $k$ products of the exponential of pair coupled-cluster double excitation operators (pCCD), together with generalized single (S) excitation operators. We compare its performance in both efficiency of implementation and accuracy with that of the generalized UCC ansatz employing the full generalized SD excitation operators (UCCGSD), as well as with the standard ansatz employing only SD excitations (UCCSD). $k$-UpCCGSD is found to show the best scaling for quantum computing applications, requiring a circuit depth of $\mathcal O(kN)$, compared with $\mathcal O(N^3)$ for UCCGSD and $\mathcal O((N-\eta)^2 \eta)$ for UCCSD where $N$ is the number of spin orbitals and $\eta$ is the number of electrons. We analyzed the accuracy of these three ans\"atze by making classical benchmark calculations on the ground state and the first excited state of H$_4$ (STO-3G, 6-31G), H$_2$O (STO-3G), and N$_2$ (STO-3G), making additional comparisons to conventional coupled cluster methods. The results for ground states show that $k$-UpCCGSD offers a good tradeoff between accuracy and cost, achieving chemical accuracy for lower cost of implementation on quantum computers than both UCCGSD and UCCSD. Excited states are calculated with an orthogonally constrained variational quantum eigensolver approach. This is seen to generally yield less accurate energies than for the corresponding ground states. We demonstrate that using a specialized multi-determinantal reference state constructed from classical linear response calculations allows these excited state energetics to be improved

Anthropocene: its stratigraphic basis

As officers of the Anthropocene Working Group (AWG; J.Z. and C.W.) and chair of the Subcommission on Quaternary Stratigraphy (SQS; M.J.H.) of the International Commission on Stratigraphy (ICS), we note that the AWG has less power than Erle Ellis and colleagues imply (Nature 540, 192–193; 2016). Its role is merely advisory — to evaluate the Anthropocene as a formal unit in the geological timescale. Proposals must pass scrutiny by the AWG, the SQS and the ICS before being ratified by the Executive Committee of the International Union of Geological Sciences

The symmetric quasi-classical model using on-the-fly time-dependent density functional theory within the Tamm-Dancoff approximation

The primary computational challenge when simulating nonadiabatic ab initio molecular dynamics is the unfavorable compute costs of electronic structure calculations with molecular size. Simple electronic structure theories, like time-dependent density functional theory within the Tamm-Dancoff approximation (TDDFT/TDA), alleviate this cost for moderately sized molecular systems simulated on realistic time scales. Although TDDFT/TDA does have some limitations in accuracy, an appealing feature is that, in addition to including electron correlation through the use of a density functional, the cost of calculating analytic nuclear gradients and nonadiabatic coupling vectors is often computationally feasible even for moderately-sized basis sets. In this work, some of the benefits and limitations of TDDFT/TDA are discussed and analyzed with regard to its applicability as a "back-end" electronic structure method for the symmetric quasi-classical Meyer-Miller model (SQC/MM). In order to investigate the benefits and limitations of TDDFT/TDA, SQC/MM is employed to predict and analyze a prototypical example of excited-state hydrogen transfer in gas-phase malonaldehyde. Then, the ring-opening dynamics of selenophene are simulated which highlight some of the deficiencies of TDDFT/TDA. Additionally, some new algorithms are proposed that speed up the calculation of analytic nuclear gradients and nonadiabatic coupling vectors for a set of excited electronic states.Comment: 35 pages, 8 figures, 2 table

Volatile hydrocarbons inhibit methanogenic crude oil degradation

Methanogenic degradation of crude oil in subsurface sediments occurs slowly, but without the need for exogenous electron acceptors, is sustained for long periods and has enormous economic and environmental consequences. Here we show that volatile hydrocarbons are inhibitory to methanogenic oil biodegradation by comparing degradation of an artificially weathered crude oil with volatile hydrocarbons removed, with the same oil that was not weathered. Volatile hydrocarbons (nC5-nC10, methylcyclohexane, benzene, toluene, and xylenes) were quantified in the headspace of microcosms. Aliphatic (n-alkanes nC12-nC34) and aromatic hydrocarbons (4-methylbiphenyl, 3-methylbiphenyl, 2-methylnaphthalene, 1-methylnaphthalene) were quantified in the total hydrocarbon fraction extracted from the microcosms. 16S rRNA genes from key microorganisms known to play an important role in methanogenic alkane degradation (Smithella and Methanomicrobiales) were quantified by quantitative PCR. Methane production from degradation of weathered oil in microcosms was rapid (1.1 ± 0.1 μmol CH4/g sediment/day) with stoichiometric yields consistent with degradation of heavier n-alkanes (nC12-nC34). For non-weathered oil, degradation rates in microcosms were significantly lower (0.4 ± 0.3 μmol CH4/g sediment/day). This indicated that volatile hydrocarbons present in the non-weathered oil inhibit, but do not completely halt, methanogenic alkane biodegradation. These findings are significant with respect to rates of biodegradation of crude oils with abundant volatile hydrocarbons in anoxic, sulphate-depleted subsurface environments, such as contaminated marine sediments which have been entrained below the sulfate-reduction zone, as well as crude oil biodegradation in petroleum reservoirs and contaminated aquifers

A New View on Density Corrected DFT: Can One Get a Better Answer for a Good Reason?

Despite its widespread use, density functional theory (DFT) has several notable areas of failure; perhaps the most well-studied of these failures is self-interaction error (SIE). Density corrected DFT (DC-DFT) was proposed as a potential solution to systems where SIE causes traditional DFT to fail. The Hartree-Fock (HF) density is then used for cases where the DFT energy is suitable but the self-consistent density is erroneous. In this study, we investigate the utility of the higher quality orbital optimized MP2 densities in DC-DFT for barrier heights and halogen bonded complexes. For functionals such as PBE and r$^2$SCAN, find that these densities yield worse results than the HF density due to favorable cancellation between the density-driven and functional-driven errors, confirming a recent study. Error decomposition reveals functional driven error, not density driven error, to be the primary cause of inaccuracy in DFT calculations where SIE is prominent. We therefore advise caution when using HF-DFT, because the only rigorous way to remove large functional-driven errors in lower rungs of Jacob's ladder is by climbing to higher rungs that include exact exchange. We recommend that better functionals be improved by using a better density in SIE-sensitive cases. Examples support the value of this variant of DC-DFT. We also emphasize that DC-DFT potential energy surfaces have first derivative discontinuities at Coulson-Fischer points, in contrast to the second derivative discontinuities in SCF solutions

Non-orthogonal configuration interaction with single substitutions for core-excited states: An extension to doublet radicals

In this paper, we present an open-shell extension of the non-orthogonal configuration interaction singles (NOCIS) method for the calculation of core-excited states, intended for peak assignment in XAS spectra of doublet radicals. This extension requires the consideration of additional configurations due to the singly occupied open-shell orbital, and the addition of essential orbital relaxation effects is found to provide a significant improvement on standard CIS, while maintaining the desirable properties of spin purity, variationality, and size consistency. We apply this method to the calculation of core excitations for several open-shell molecules and demonstrate that it performs competitively with other available methods, despite a lack of dynamic correlation. In particular, relative to CVS-ADC(2)-x, RMS error is reduced by a factor of 6 over usual orthogonal CIS and is comparable to time-dependent density functional theory with the best short-range corrected functionals

Initiating Molecular Growth in the Interstellar Medium via Dimeric Complexes of Observed Ions and Molecules

A feasible initiation step for particle growth in the interstellar medium (ISM) is simulated by means of ab quantum chemistry methods. The systems studied are dimer ions formed by pairing nitrogen containing small molecules known to exist in the ISM with ions of unsaturated hydrocarbons or vice versa. Complexation energies, structures of ensuing complexes and electronic excitation spectra of the encounter complexes are estimated using various quantum chemistry methods. Moller-Plesset perturbation theory (MP2, Z-averaged perturbation theory (ZAP2), coupled cluster singles and doubles with perturbative triples corrections (CCSD(T)), and density functional theory (DFT) methods (B3LYP) were employed along with the correlation consistent cc-pVTZ and aug-cc-pVTZ basis sets. Two types of complexes are predicted. One type of complex has electrostatic binding with moderate (7-20 kcal per mol) binding energies, that are nonetheless significantly stronger than typical van der Waals interactions between molecules of this size. The other type of complex develops strong covalent bonds between the fragments. Cyclic isomers of the nitrogen containing complexes are produced very easily by ion-molecule reactions. Some of these complexes show intense ultraviolet visible spectra for electronic transitions with large oscillator strengths at the B3LYP, omegaB97, and equations of motion coupled cluster (EOM-CCSD) levels. The open shell nitrogen containing carbonaceous complexes especially exhibit a large oscillator strength electronic transition in the visible region of the electromagnetic spectrum

Formal ratification of the GSSP for the base of the Calabrian Stage (second stage of the Pleistocene Series, Quaternary System)

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