Analytic gradients for relativistic exact-two-component equation-of-motion coupled-cluster singles and doubles method.

A first implementation of analytic gradients for spinor-based relativistic equation-of-motion coupled-cluster singles and doubles method using an exact two-component Hamiltonian augmented with atomic mean-field spin-orbit integrals is reported. To demonstrate its applicability, we present calculations of equilibrium structures and harmonic vibrational frequencies for the electronic ground and excited states of the radium mono-amide molecule (RaNH2) and the radium mono-methoxide molecule (RaOCH3). Spin-orbit coupling is shown to quench Jahn-Teller effects in the first excited state of RaOCH3, resulting in a C3v equilibrium structure. The calculations also show that the radium atoms in these molecules serve as efficient optical cycling centers.

Geometry optimizations with spinor-based relativistic coupled-cluster theory.

Development of analytic gradients for relativistic coupled-cluster singles and doubles augmented with a non-iterative triples [CCSD(T)] method using an all-electron exact two-component Hamiltonian with atomic mean-field spin-orbit integrals (X2CAMF) is reported. This enables efficient CC geometry optimizations with spin-orbit coupling included in orbitals. The applicability of the implementation is demonstrated using benchmark X2CAMF-CCSD(T) calculations of equilibrium structures and harmonic vibrational frequencies for methyl halides, CH3X (X = Br, I, and At), as well as calculations of rotational constants and infrared spectrum for RaSH+, a radioactive molecular ion of interest to spectroscopic study.

Aminomethylpyridine isomers functionalized cellulose microspheres for TcO4-/ReO4- uptake: Structure-properties relationship and their application in different aquatic systems.

Technetium-99 (99Tc) is a long-lived radioactive nuclide that poses great threat to environment, hence selective removal of 99Tc from aquatic system is always an issue. Aminomethylpyridine (AMP) equipped with pyridine and amino, is a promising receptor for TcO4- and its surrogate ReO4-, thus it is of interest to explore and understand the structure-properties relationship of ReO4- adsorption related to n-AMP structure that differ in amino methyl position. In this work, three n-AMP functionalized cellulose microspheres (n-AMPR, n = 2, 3, 4) were synthesized and employed for TcO4-/ReO4- uptake. The effect of aminomethyl position on adsorption properties of n-AMPR for ReO4- were investigated and compared. Adsorption kinetics and adsorption isotherm showed that adsorption speed and adsorption capacity were in order of 3-AMPR > 2-AMPR > 4-AMPR. DFT calculation verified that the adsorption of ReO4- by n-AMPR was attributed to electrostatic interaction and hydrogen bonding interaction, the order of adsorption abilities of n-AMPR was due to that steric effect and hydrogen bond collaborated in stabilizing n-AMPR-ReO4- complexes. The column experiments demonstrated that 3-AMPR can be selectively remove ReO4- from simulated groundwater. More importantly, 99Tc column experiments showed that 3-AMPR had a better ability for actual radioactive TcO4-.

Quadratic Unitary Coupled-Cluster Singles and Doubles Scheme: Efficient Implementation, Benchmark Study, and Formulation of an Extended Version.

An efficient implementation of the quadratic unitary coupled-cluster singles and doubles (qUCCSD) scheme for calculations of electronic ground and excited states using an unrestricted molecular spin-orbital formulation and an efficient tensor contraction library is reported. The accuracy of the qUCCSD scheme and the efficiency of the present implementation are demonstrated using extensive benchmark calculations of excitation energies and an application to S0 → S1 vertical excitation energies for cis- and trans-4a,4b-dihydrotriphenylene. The qUCCSD scheme has been shown to provide improved excitation energies compared with the UCC3 scheme formulated based on perturbation theory. A UCC truncation scheme that can provide excitation energies correct through the fourth order is also presented to further improve the accuracy of the qUCCSD scheme.

Unitary coupled-cluster based self-consistent polarization propagator theory: A quadratic unitary coupled-cluster singles and doubles scheme.

The development of a quadratic unitary coupled-cluster singles and doubles (qUCCSD) based self-consistent polarization propagator method is reported. We present a simple strategy for truncating the commutator expansion of the unitary version of coupled-cluster transformed Hamiltonian H̄. The qUCCSD method for the electronic ground state includes up to double commutators for the amplitude equations and up to cubic commutators for the energy expression. The qUCCSD excited-state eigenvalue equations include up to double commutators for the singles-singles block of H̄, single commutators for the singles-doubles and doubles-singles blocks, and the bare Hamiltonian for the doubles-doubles block. Benchmark qUCCSD calculations of the ground-state properties and excitation energies for representative molecules demonstrate significant improvement of the accuracy and robustness over the previous UCC3 scheme derived using Møller-Plesset perturbation theory.

Photoelectron Spectroscopic and ab Initio Computational Studies of the Anion, HThO.

The synergetic combination of anion photoelectron spectroscopy and high-level relativistic coupled-cluster calculations was employed to study the anion, HThO-. The atomic connectivity of this anion was found to be HThO- and not ThOH-. Vibrational and electronic energy spacings in the HThO- photoelectron spectrum were measured and calculated, with good agreement between them being found. Computations yielded electronic energies and equilibrium structures as well as enabling orbital analyses. The adiabatic electron affinity (EAa) of HThO was determined to be 1.297 ± 0.035 eV.

Analytic evaluation of energy first derivatives for spin-orbit coupled-cluster singles and doubles augmented with noniterative triples method: General formulation and an implementation for first-order properties.

A formulation of analytic energy first derivatives for the coupled-cluster singles and doubles augmented with noniterative triples [CCSD(T)] method with spin-orbit coupling included at the orbital level and an implementation for evaluation of first-order properties are reported. The standard density-matrix formulation for analytic CC gradient theory adapted to complex algebra has been used. The orbital-relaxation contributions from frozen core, occupied, virtual, and frozen virtual orbitals to analytic spin-orbit CCSD(T) gradients are fully taken into account and treated efficiently, which is of importance to calculations of heavy elements. Benchmark calculations of first-order properties including dipole moments and electric-field gradients using the corresponding exact two-component property integrals are presented for heavy-element containing molecules to demonstrate the applicability and usefulness of the present analytic scheme.

Recent developments in the PySCF program package.

PySCF is a Python-based general-purpose electronic structure platform that supports first-principles simulations of molecules and solids as well as accelerates the development of new methodology and complex computational workflows. This paper explains the design and philosophy behind PySCF that enables it to meet these twin objectives. With several case studies, we show how users can easily implement their own methods using PySCF as a development environment. We then summarize the capabilities of PySCF for molecular and solid-state simulations. Finally, we describe the growing ecosystem of projects that use PySCF across the domains of quantum chemistry, materials science, machine learning, and quantum information science.

Third-Order Unitary Coupled Cluster (UCC3) for Excited Electronic States: Efficient Implementation and Benchmarking.

The efficient implementation of the third-order unitary coupled-cluster scheme (UCC3) for the calculation of excited electronic states is reported. The UCC3 scheme and its second-order UCC2 variant have been benchmarked and compared to Jacquemin's recently introduced, as well as Thiel's well-established, benchmark sets for excitation energies and oscillator strengths. For the latter, the calculation of 134 excited singlet and 71 excited triplet states of 28 small- to medium-sized organic molecules has revealed that UCC2 exhibits a mean error and standard deviation of 0.36 ± 0.41 eV for singlet states and 0.22 ± 0.21 eV for triplet states, whereas UCC3 revealed an accuracy of 0.06 ± 0.27 eV for singlet and -0.22 ± 0.15 eV for triplet states. In addition, the oscillator strengths obtained with effective transition moments correct through second order in perturbation theory are in very good agreement with literature data.

Hetero-site Double Core Ionization Energies with Sub-electronvolt Accuracy from Delta-Coupled-Cluster Calculations.

Benchmark scalar-relativistic delta-coupled-cluster calculations of hetero-site double core ionization energies of small molecules containing second-row elements are reported. The present study has focused on the high-spin triplet components of two-site double core-ionized states, which are single reference in character and consistent with the use of standard coupled-cluster methods. Contributions to computed double core ionization energies from electron-correlation and basis-set effects as well as corrections to the core-valence separation approximation have been analyzed. On the basis of systematic convergence of computational results with respect to these effects, delta-coupled-cluster calculations have been shown to be capable of providing accurate double core ionization energies with remaining errors estimated to be below 0.3 eV, and thus they are recommended for use to facilitate experimental studies of two-site double core-ionized states that are involved in X-ray pump/X-ray probe studies of electronic and molecular dynamics following inner shell ionization or excitation.

Synergistic antibacterial mechanism of Bi2Te3 nanoparticles combined with the ineffective ß-lactam antibiotic cefotaxime against methicillin-resistant Staphylococcus aureus.

Methicillin-resistant Staphylococcus aureus (MRSA) infections have become a serious threat to public health because traditional antibiotics are less efficient. Here, we developed a simple and efficient combination of Bi2Te3 nanoparticles (NPs) with ß-lactam antibiotics cefotaxime (CTX), which presented significant synergistic antibacterial activity against MRSA. The minimal inhibitory concentration of CTX decreased from 256 to 32 µg/mL in the presence of 8 µg/mL Bi2Te3 NPs. The results of cell membrane potential and cellular K+ content measurements demonstrated that the destruction of membrane functions is a factor in the synergistic mechanism. Furthermore, the induction of cellular reactive oxygen species generation, inhibition of ß-lactamases induced by CTX and direct damage to the cell structure constituted other factors of the synergistic mechanism. These observations suggest that reviving the efficacy of ineffective ß-lactam antibiotic CTX by Bi2Te3 NPs may be a potentially effective therapeutic strategy to overcome refractory MRSA infections.

Exact two-component equation-of-motion coupled-cluster singles and doubles method using atomic mean-field spin-orbit integrals.

A new semi-atomic-orbital- based algorithm for a two-component spin-orbit (SO) equation-of-motion coupled-cluster singles and doubles (EOM-CCSD) method using mean-field SO integrals is reported. The new algorithm removes the major computational bottlenecks of a SO-EOM-CCSD calculation associated with the evaluation, storage, and processing of the H¯ab,cd elements in the similarity-transformed Hamiltonian involving four virtual orbital labels. The partial recovery of spin symmetry in the present algorithm reduces the storage requirement by an order of magnitude and the floating point operation count for the evaluation of the ladder-like term by a factor of three to four. EOM-CCSD calculations of excited states in the triiodide ion (I3 -) using the exact two-component Hamiltonian in combination with atomic mean-field SO integrals (X2CAMF) are reported as a validation of the implementation and also as a demonstration of the capability of the new algorithm to correlate extended virtual spaces. X2CAMF-EOM-CCSD calculations of the ground and excited states in As2, Sb2, and Bi2 are also presented and compared with the available experimental studies. An analysis based on the computed spectroscopic constants as well as the compositions of the excited-state wavefunctions strongly supports a new assignment for the lowest 2u and 0u - levels in the photoelectron spectrum of Bi2.

Benchmark Calculations of K-Edge Ionization Energies for First-Row Elements Using Scalar-Relativistic Core-Valence-Separated Equation-of-Motion Coupled-Cluster Methods.

Benchmark scalar-relativistic core-valence-separated (CVS) equation-of-motion coupled-cluster ionization potential (EOMIP-CC) calculations of 21 K-edge ionization energies of C, O, N, and F in 14 molecules are reported. The CVS-EOMIP-CC methods are shown to be numerically more stable and more accurate than the parent EOMIP-CC methods, even when the calculations using the latter can be tightly converged. The superior performance of the CVS scheme is attributed to the exclusion of spurious couplings between core-ionized states and valence continuum states. Systematic improvement of computed K-edge ionization energies within the CVS-EOMIP-CC hierarchy, including the CC singles and doubles (CCSD) method, the CC singles, doubles, and triples (CCSDT) method, and the CC singles, doubles, triples, and quadruples (CCSDTQ) method, is demonstrated, with CCSDTQ yielding essentially quantitative results. Maximum absolute deviations between computed and experimental results amount to 2.54 eV for CCSD/cc-pCVQZ, 0.54 eV for CCSDT/cc-pCVQZ, and 0.23 eV for CCSDT/cc-pCVQZ augmented with quadruples contributions using the cc-pVTZ basis sets. The corresponding standard deviations are 1.91 eV for CCSD/cc-pCVQZ, 0.18 eV for CCSDT/cc-pCVQZ, and 0.10 eV for CCSDT/cc-pCVQZ augmented with quadruples contributions using the cc-pVTZ basis sets. Finally, CVS-EOMIP-CCSDT/cc-pCVTZ calculations of core ionization energies in CH3CN and CH3NC are reported, and experimental reinvestigation of carbon 1s ionization energies in CH3CN is suggested.

Unitary coupled-cluster based self-consistent polarization propagator theory: A third-order formulation and pilot applications.

In this article, the development of a third-order self-consistent polarization propagator method based on unitary coupled-cluster (UCC) parametrization of the ground-state wavefunction and the excitation manifold comprising unitary-transformed excitation operators, hereafter referred to as UCC3, is reported. The UCC3 method is designed to provide excitation energies correct up to the third order for excited states dominated by single excitations. An expansion for the UCC transformed Hamiltonian involving Bernoulli numbers as expansion coefficients is adopted in the derivation of UCC3 working equations. Interestingly, UCC-based polarization propagator theory offers an alternative derivation for the strict version of the third-order algebraic diagrammatic construction [ADC(3)-s] method. The UCC3 results for the excitation energies of excited states in H2O, HF, N2, Ne, CH2, BH, and C2 molecules are compared with benchmark full configuration interaction values as well as ADC(3) and equation-of-motion coupled-cluster singles and doubles results to demonstrate the accuracy of the UCC3 method. UCC-based self-consistent polarization propagator theory appears to be a promising framework for developing non-perturbative hermitian formulations for treating electronically excited states.

An atomic mean-field spin-orbit approach within exact two-component theory for a non-perturbative treatment of spin-orbit coupling.

An atomic mean-field (AMF) spin-orbit (SO) approach within exact two-component theory (X2C) is reported, thereby exploiting the exact decoupling scheme of X2C, the one-electron approximation for the scalar-relativistic contributions, the mean-field approximation for the treatment of the two-electron SO contribution, and the local nature of the SO interactions. The Hamiltonian of the proposed SOX2CAMF scheme comprises the one-electron X2C Hamiltonian, the instantaneous two-electron Coulomb interaction, and an AMF SO term derived from spherically averaged Dirac-Coulomb Hartree-Fock calculations of atoms; no molecular relativistic two-electron integrals are required. Benchmark calculations for bond lengths, harmonic frequencies, dipole moments, and electric-field gradients for a set of diatomic molecules containing elements across the periodic table show that the SOX2CAMF scheme offers a balanced treatment for SO and scalar-relativistic effects and appears to be a promising candidate for applications to heavy-element containing systems. SOX2CAMF coupled-cluster calculations of molecular properties for bismuth compounds (BiN, BiP, BiF, BiCl, and BiI) are also presented and compared with experimental results to further demonstrate the accuracy and applicability of the SOX2CAMF scheme.

Two-component relativistic coupled-cluster methods using mean-field spin-orbit integrals.

A novel implementation of the two-component spin-orbit (SO) coupled-cluster singles and doubles (CCSD) method and the CCSD augmented with the perturbative inclusion of triple excitations [CCSD(T)] method using mean-field SO integrals is reported. The new formulation of SO-CCSD(T) features an atomic-orbital-based algorithm for the particle-particle ladder term in the CCSD equation, which not only removes the computational bottleneck associated with the large molecular-orbital integral file but also accelerates the evaluation of the particle-particle ladder term by around a factor of 4 by taking advantage of the spin-free nature of the instantaneous electron-electron Coulomb interaction. Benchmark calculations of the SO splittings for the thallium atom and a set of diatomic 2Π radicals as well as of the bond lengths and harmonic frequencies for a set of closed-shell diatomic molecules are presented. The basis-set and core-correlation effects in the calculations of these properties have been carefully analyzed.

Evaluating Electronic Couplings for Excited State Charge Transfer Based on Maximum Occupation Method ΔSCF Quasi-Adiabatic States.

Electronic couplings of charge-transfer states with the ground state and localized excited states at the donor/acceptor interface are crucial parameters for controlling the dynamics of exciton dissociation and charge recombination processes in organic solar cells. Here we propose a quasi-adiabatic state approach to evaluate electronic couplings through combining maximum occupation method (mom)-ΔSCF and state diabatization schemes. Compared with time-dependent density functional theory (TDDFT) using global hybrid functional, mom-ΔSCF is superior to estimate the excitation energies of charge-transfer states; moreover it can also provide good excited electronic state for property calculation. Our approach is hence reliable to evaluate electronic couplings for excited state electron transfer processes, which is demonstrated by calculations on a typical organic photovoltaic system, oligothiophene/perylenediimide complex.

GdF3 as a promising phosphopeptide affinity probe and dephospho-labelling medium: experiments and theoretical explanation.

Bone-like GdF3 was synthesized and applied for phosphopeptide enrichment for the first time. As a new kind of efficient phosphopeptide affinity probe, GdF3 exhibits high efficiency in the mediation of the dephosphorylation reaction. In addition, DFT calculations were introduced to theoretically explain the unique property of GdF3 compared to GdPO4, which is promising and can be potentially significant in protein phosphorylation research.

Towards understanding the color change of 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide during gamma irradiation: an experimental and theoretical study.

The application of room-temperature ionic liquids (RTILs) in nuclear spent fuel recycling requires a comprehensive knowledge of radiation effects on RTILs. Although preliminary studies indicate a relatively high radiation stability of RTILs, little attention is paid to the color change of RTILs, an obvious phenomenon of RTILs during irradiation. In this paper, we have investigated radiation-induced darkening and decoloration of 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ([BMIm][NTf2]), an ionic liquid representing the most popular class of RTILs, by means of UV-Vis analysis and time-dependent density functional theory calculations. Based on the experimental and computational results, it is proposed that the color change of [BMIm][NTf2] upon irradiation originates from the formation of double bonds in the aliphatic chains of pristine organic cations (or radiolytic products of RTILs) and various associated species containing these "double-bond products". This work sheds light on the understanding of the radiation-induced color change of RTILs.

Photoexcitation of Light-Harvesting C-P-C60 Triads: A FLMO-TD-DFT Study.

UNLABELLED: The recently proposed linear-scaling time-dependent density functional theory (TD-DFT) [ J. Chem. THEORY: Comput. 2011 , 7 , 3643 ] is employed to capture more than 300 low-lying excited states for three light-harvesting C-P-C60 triads composed of ß-carotenoid polyene (C), diaryl-based porphyrin (P), and pyrrole-fullerene (C60). The simulated optical absorption spectra are grossly in good agreement with experimental observations. To gain insights on the structure-property relations, both top-down and bottom-up analyses of the excited states are made in terms of the underlying fragment localized molecular orbitals (FLMO). A maximum occupation method is further proposed for finding excited-state solutions of self-consistent-field equations and is applied to long-range charge-transfer states that cannot be described by TD-DFT with pure density functionals.