Characterization of Singlet Ground and Low-Lying Electronic Excited States of Phosphaethyne and Isophosphaethyne

The singlet ground _X˜ 1_+_ and excited _1_− , 1__ states of HCP and HPC have been systematically investigated using ab initio molecular electronic structure theory. For the ground state, geometries of the two linear stationary points have been optimized and physical properties have been predicted utilizing restricted self-consistent field theory, coupled cluster theory with single and double excitations _CCSD_, CCSD with perturbative triple corrections _CCSD_T__, and CCSD with partial iterative triple excitations _CCSDT-3 and CC3_. Physical properties computed for the global minimum _X˜ 1_+HCP_ include harmonic vibrational frequencies with the cc-pV5Z CCSD_T_ method of _1=3344 cm−1, _2=689 cm−1, and _3=1298 cm−1. Linear HPC, a stationary point of Hessian index 2, is predicted to lie 75.2 kcal mol−1 above the global minimum HCP. The dissociation energy D0_HCP_X˜ 1_+_→H_2S_+CP_X 2_+__ of HCP is predicted to be 119.0 kcal mol−1, which is very close to the experimental lower limit of 119.1 kcal mol−1. Eight singlet excited states were examined and their physical properties were determined employing three equation-of-motion coupled cluster methods _EOM-CCSD, EOM-CCSDT-3, and EOM-CC3_. Four stationary points were located on the lowest-lying excited state potential energy surface, 1_− →1A_, with excitation energies Te of 101.4 kcal mol−1_1A_ HCP_, 104.6 kcal mol−1_1_− HCP_, 122.3 kcal mol−1_1A_ HPC_, and 171.6 kcal mol−1_1_− HPC_ at the cc-pVQZ EOM-CCSDT-3 level of theory. The physical properties of the 1A_ state with a predicted bond angle of 129.5° compare well with the experimentally reported first singlet state _A˜ 1A__. The excitation energy predicted for this excitation is T0=99.4 kcal mol−1_34 800 cm−1 , 4.31 eV_, in essentially perfect agreement with the experimental value of T0=99.3 kcal mol−1_34 746 cm−1 ,4.308 eV_. For the second lowest-lying excited singlet surface, 1_→1A_, four stationary points were found with Te values of 111.2 kcal mol−1 _21A_ HCP_, 112.4 kcal mol−1 _1_ HPC_, 125.6 kcal mol−1_2 1A_ HCP_, and 177.8 kcal mol−1_1_ HPC_. The predicted CP bond length and frequencies of the 2 1A_ state with a bond angle of 89.8° _1.707 Å, 666 and 979 cm−1_ compare reasonably well with those for the experimentally reported C ˜ 1A_ state _1.69 Å, 615 and 969 cm−1_. However, the excitation energy and bond angle do not agree well: theoretical values of 108.7 kcal mol−1 and 89.8° versus experimental values of 115.1 kcal mol−1 and 113°

Coupled Cluster Externally Corrected by Adaptive Configuration Interaction

An externally corrected coupled cluster (CC) method, where an adaptive configuration interaction (ACI) wave function provides the external cluster amplitudes, named ACI-CC, is presented. By exploiting the connection between configuration interaction and coupled cluster through cluster analysis, the higher-order T3 and T4 terms obtained from ACI are used to augment the T1 and T2 amplitude equations from traditional coupled cluster. These higher-order contributions are kept frozen during the coupled cluster iterations and do not contribute to an increased cost with respect to CCSD. We have benchmarked this method on three closed-shell systems: beryllium dimer, carbonyl oxide, and cyclobutadiene, with good results compared to other corrected coupled cluster methods. In all cases, the inclusion of these external corrections improved upon the "gold standard" CCSD(T) results, indicating that ACI-CCSD(T) can be used to assess strong correlation effects in a system and as an inexpensive starting point for more complex external corrections

Psi4

Psi4 is an ab initio electronic structure program providing methods such as Hartree-Fock, density functional theory, configuration interaction, and coupled-cluster theory. The 1.1 release represents a major update meant to automate complex tasks, such as geometry optimization using complete-basis-set extrapolation or focal-point methods. Conversion of the top-level code to a Python module means that Psi4 can now be used in complex workflows alongside other Python tools. Several new features have been added with the aid of libraries providing easy access to techniques such as density fitting, Cholesky decomposition, and Laplace denominators. The build system has been completely rewritten to simplify interoperability with independent, reusable software components for quantum chemistry. Finally, a wide range of new theoretical methods and analyses have been added to the code base, including functional-group and open-shell symmetry adapted perturbation theory, density-fitted coupled cluster with frozen natural orbitals, orbital-optimized perturbation and coupled-cluster methods (e.g., OO-MP2 and OO-LCCD), density-fitted multiconfigurational self-consistent field, density cumulant functional theory, algebraic-diagrammatic construction excited states, improvements to the geometry optimizer, and the "X2C" approach to relativistic corrections, among many other improvements

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Effect of remote ischaemic conditioning on clinical outcomes in patients with acute myocardial infarction (CONDI-2/ERIC-PPCI): a single-blind randomised controlled trial.

BACKGROUND: Remote ischaemic conditioning with transient ischaemia and reperfusion applied to the arm has been shown to reduce myocardial infarct size in patients with ST-elevation myocardial infarction (STEMI) undergoing primary percutaneous coronary intervention (PPCI). We investigated whether remote ischaemic conditioning could reduce the incidence of cardiac death and hospitalisation for heart failure at 12 months. METHODS: We did an international investigator-initiated, prospective, single-blind, randomised controlled trial (CONDI-2/ERIC-PPCI) at 33 centres across the UK, Denmark, Spain, and Serbia. Patients (age >18 years) with suspected STEMI and who were eligible for PPCI were randomly allocated (1:1, stratified by centre with a permuted block method) to receive standard treatment (including a sham simulated remote ischaemic conditioning intervention at UK sites only) or remote ischaemic conditioning treatment (intermittent ischaemia and reperfusion applied to the arm through four cycles of 5-min inflation and 5-min deflation of an automated cuff device) before PPCI. Investigators responsible for data collection and outcome assessment were masked to treatment allocation. The primary combined endpoint was cardiac death or hospitalisation for heart failure at 12 months in the intention-to-treat population. This trial is registered with ClinicalTrials.gov (NCT02342522) and is completed. FINDINGS: Between Nov 6, 2013, and March 31, 2018, 5401 patients were randomly allocated to either the control group (n=2701) or the remote ischaemic conditioning group (n=2700). After exclusion of patients upon hospital arrival or loss to follow-up, 2569 patients in the control group and 2546 in the intervention group were included in the intention-to-treat analysis. At 12 months post-PPCI, the Kaplan-Meier-estimated frequencies of cardiac death or hospitalisation for heart failure (the primary endpoint) were 220 (8·6%) patients in the control group and 239 (9·4%) in the remote ischaemic conditioning group (hazard ratio 1·10 [95% CI 0·91-1·32], p=0·32 for intervention versus control). No important unexpected adverse events or side effects of remote ischaemic conditioning were observed. INTERPRETATION: Remote ischaemic conditioning does not improve clinical outcomes (cardiac death or hospitalisation for heart failure) at 12 months in patients with STEMI undergoing PPCI. FUNDING: British Heart Foundation, University College London Hospitals/University College London Biomedical Research Centre, Danish Innovation Foundation, Novo Nordisk Foundation, TrygFonden

Quadratically convergent algorithm for orbital optimization in the orbital-optimized coupled-cluster doubles method and in orbital-optimized second-order Møller-Plesset perturbation theory

© 2011 American Institute of Physics. The electronic version of this article is the complete one and can be found at: http://dx.doi.org/10.1063/1.3631129DOI: 10.1063/1.3631129Using a Lagrangian-based approach, we present a more elegant derivation of the equations necessary for the variational optimization of the molecular orbitals (MOs) for the coupled-cluster doubles (CCD) method and second-order Møller-Plesset perturbation theory (MP2). These orbital-optimized theories are referred to as OO-CCD and OO-MP2 (or simply “OD” and “OMP2” for short), respectively. We also present an improved algorithm for orbital optimization in these methods. Explicit equations for response density matrices, the MO gradient, and the MO Hessian are reported both in spin-orbital and closed-shell spin-adapted forms. The Newton-Raphson algorithm is used for the optimization procedure using the MO gradient and Hessian. Further, orbital stability analyses are also carried out at correlated levels. The OD and OMP2 approaches are compared with the standard MP2, CCD, CCSD, and CCSD(T) methods. All these methods are applied to H₂O, three diatomics, and the O₄⁺ molecule. Results demonstrate that the CCSD and OD methods give nearly identical results for H₂O and diatomics; however, in symmetry-breaking problems as exemplified by O₄⁺, the OD method provides better results for vibrational frequencies. The OD method has further advantagesover CCSD: its analytic gradients are easier to compute since there is no need to solve the coupledperturbed equations for the orbital response, the computation of one-electron properties are easier because there is no response contribution to the particle density matrices, the variational optimized orbitals can be readily extended to allow inactive orbitals, it avoids spurious second-order poles in its response function, and its transition dipole moments are gauge invariant. The OMP2 has these same advantages over canonical MP2, making it promising for excited state properties via linear response theory. The quadratically convergent orbital-optimization procedure converges quickly for OMP2, and provides molecular properties that are somewhat different than those of MP2 for most of the test cases considered (although they are similar for H₂O). Bond lengths are somewhat longer, and vibrational frequencies somewhat smaller, for OMP2 compared to MP2. In the difficult case of O₄⁺, results for several vibrational frequencies are significantly improved in going from MP2 to OMP2

Large-scale symmetry-adapted perturbation theory computations via density fitting and Laplace transformation techniques: Investigating the fundamental forces of DNA-intercalator interactions

© 2011 American Institute of Physics. The electronic version of this article is the complete one and can be found at: http://dx.doi.org/10.1063/1.3656681DOI: 10.1063/1.3656681Symmetry-adapted perturbation theory (SAPT) provides a means of probing the fundamental nature of intermolecular interactions. Low-orders of SAPT (here, SAPT0) are especially attractive since they provide qualitative (sometimes quantitative) results while remaining tractable for large systems. The application of density fitting and Laplace transformation techniques to SAPT0 can significantly reduce the expense associated with these computations and make even larger systems accessible. We present new factorizations of the SAPT0 equations with density-fitted two-electron integrals and the first application of Laplace transformations of energy denominators to SAPT. The improved scalability of the DF-SAPT0 implementation allows it to be applied to systems with more than 200 atoms and 2800 basis functions. The Laplace-transformed energy denominators are compared to analogous partial Cholesky decompositions of the energy denominator tensor. Application of our new DF-SAPT0 program to the intercalation of DNA by proflavine has allowed us to determine the nature of the proflavine-DNA interaction. Overall, the proflavine-DNA interaction contains important contributions from both electrostatics and dispersion. The energetics of the intercalator interaction are are dominated by the stacking interactions (two-thirds of the total), but contain important contributions from the intercalator-backbone interactions. It is hypothesized that the geometry of the complex will be determined by the interactions of the intercalator with the backbone, because by shifting toward one side of the backbone, the intercalator can form two long hydrogen-bonding type interactions. The long-range interactions between the intercalator and the next-nearest base pairs appear to be negligible, justifying the use of truncated DNA models in computational studies of intercalation interaction energies

The barrier height, unimolecular rate constant, and lifetime for the dissociation of HN2

Although never spectroscopically identified in the laboratory, hydrogenated nitrogen (HN2) is thought to be an important species in combustion chemistry. The classical barrier height (10.6 +/- 0.2 kcal mol(-1)) and exothermicity (3.6 +/- 0.2 kcal mol(-1)) for the HN2 -> N-2+H reaction are predicted by high level ab initio quantum mechanical methods [up to CCSDT(Q)]. Total energies are extrapolated to the complete basis set limit applying the focal point analysis. Zero-point vibrational energies are computed using fundamental (anharmonic) frequencies obtained from a quartic force field. Relativistic and diagonal Born-Oppenheimer corrections are also taken into account. The quantum mechanical barrier with these corrections is predicted to be 6.4 +/- 0.2 kcal mol(-1) and the reaction exothermicity to be 8.8 +/- 0.2 kcal mol(-1). The importance of these parameters for the thermal NOx decomposition (De-NOx) process is discussed. The unimolecular rate constant for dissociation of the HN2 molecule and its lifetime are estimated by canonical transition-state theory and Rice-Ramsperger-Kassel-Marcus theory. The lifetime of the HN2 molecule is here estimated to be 2.8x10(-10) s at room temperature. Our result is in marginal agreement with the latest experimental kinetic modeling studies (tau=1.5x10(-8) s), albeit consistent with the very rough experimental upper limit (tau < 0.5 mu s). For the dissociation reaction, kinetic isotope effects are investigated. Our analysis demonstrates that the DN2 molecule has a longer lifetime than the HN2 molecule. Thus, DN2 might be more readily identified experimentally. The ionization potential of the HN2 molecule is determined by analogous high level ab initio methods and focal point analysis. The adiabatic IP of HN2 is predicted to be 8.19 +/- 0.05 eV, in only fair agreement with the experimental upper limit of 7.92 eV deduced from sychrothon-radiation-based photoionization mass spectrometry

Reaction Energetics for the Abstraction Process C₂H₃ + H₂ → C₂H₄ + H

The fundamentally important combustion reaction of vinyl radical with hydrogen has been studied in the laboratory by at least five experimental groups. Herein, the reaction C₂H₃ + H₂ → C₂H₄ + H has been examined using focal-point analysis. Molecular energies were determined from extrapolations to the complete basis-set limit using correlation-consistent basis sets (cc-pVTZ, cc-pVQZ, and cc-pV5Z) and coupled-cluster theory with single and double excitations (CCSD), perturbative triples [CCSD(T)], full triples [CCSDT], and perturbative quadruples [CCSDT(Q)]. Reference geometries were optimized at the all-electron CCSD(T)/cc-pCVQZ level. Computed energies were also corrected for relativistic effects and the Born–Oppenheimer approximation. The activation energy for hydrogen abstraction is predicted to be 9.65 kcal mol^–1, and the overall reaction is predicted to be exothermic by 5.65 kcal mol^–1. Natural resonance theory (NRT) analysis was performed to verify the reaction pathway and describe bond-breaking and bond-forming events along the reaction coordinate