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Calculating molecular properties using quantum devices can be performed through the quantum linear response (qLR) or, equivalently, the quantum equation of motion (qEOM) formulations. Different parameterizations of qLR and qEOM are available, namely naïve, projected, self-consistent, and state-transfer. In the naïve and projected parameterizations, the metric is not the identity, and we show that it depends on redundant orbital rotations. This dependency may lead to divergences in the excitation energies for certain choices of the redundant orbital rotation parameters in an idealized noiseless setting. Furthermore, this leads to a significant variance when calculations include statistical noise from finite quantum sampling. [ABSTRACT FROM AUTHOR]

In this paper, benchmark results are presented on the calculation of vertical electronic excitation energies using a long-range second-order polarization propagator approximation (SOPPA) description with a short-range density functional theory description based on the Perdew–Burke–Ernzerhof (PBE) functional. The excitation energies are investigated for 132 singlet states and 71 triplet states across 28 medium-sized organic molecules. The results show that overall SOPPA-srPBE always performs better than PBE and that SOPPA-srPBE performs better than SOPPA for singlet states, but slightly worse than SOPPA for triplet states when CC3 results are the reference values. [ABSTRACT FROM AUTHOR]

We formulate and implement the Variational Quantum Eigensolver Self Consistent Field (VQE-SCF) algorithm in combination with polarizable embedding (PE), thereby extending PE to the regime of quantum computing. We test the resulting algorithm, PE-VQE-SCF, on quantum simulators and demonstrate that the computational stress on the quantum device is only slightly increased in terms of gate counts compared to regular VQE-SCF. On the other hand, no increase in shot noise was observed. We illustrate how PE-VQE-SCF may lead to the modeling of real chemical systems using a simulation of the reaction barrier of the Diels–Alder reaction between furan and ethene as an example. [ABSTRACT FROM AUTHOR]

In this study, the performance of the doubles-corrected higher random-phase approximation [HRPA(D)] has been investigated in calculations of nuclear magnetic resonance spin–spin coupling constants (SSCCs) for 58 molecules with the experimental values used as the reference values. HRPA(D) is an approximation to the second-order polarization propagator approximation (SOPPA) and is, therefore, computationally less expensive than SOPPA. HRPA(D) performs comparable and sometimes even better than SOPPA, and therefore, when calculating SSCCs, it should be considered as an alternative to SOPPA. Furthermore, it was investigated whether a coupled-cluster singles, doubles and perturbative triples [CCSD(T)] or Møller-Plesset second order (MP2) geometry optimization was optimal for a SOPPA and a HRPA(D) SSCC calculation for eight smaller molecules. CCSD(T) is the optimal geometry optimization for the SOPPA calculation, and MP2 was optimal for HRPA(D) SSCC calculations. [ABSTRACT FROM AUTHOR]

Thiolate containing mercury(II) complexes of the general formula [Hg(SR) n] 2−n have been of great interest since the toxicity of mercury was recognized. 199Hg nuclear magnetic resonance spectroscopy (NMR) is a powerful tool for characterization of mercury complexes. In this work, the Hg shielding constants in a series of [Hg(SR) n] 2−n complexes are therefore investigated computationally with particular emphasis on their geometry dependence. Geometry optimizations and NMR chemical shift calculations are performed at the density functional theory (DFT) level with both the zeroth‐order regular approximation (ZORA) and four‐component relativistic methods. The four exchange‐correlation (XC) functionals PBE0, PBE, B3LYP, and BLYP are used in combination with either Dyall's Gaussian‐type (GTO) or Slater‐type orbitals (STOs) basis sets. Comparing ZORA and four‐component calculations, one observes that the calculated shielding constants for a given molecular geometry have a constant difference of ∼1070 ppm. This confirms that ZORA is an acceptable relativistic method to compute NMR chemical shifts. The combinations of four‐component/PBE0/v3z and ZORA/PBE0/QZ4P are applied to explore the geometry dependence of the isotropic shielding. For a given coordination number, the distance between mercury and sulfur is the key factor affecting the shielding constant, while changes in bond and dihedral angles and even different side groups have relatively little impact. [ABSTRACT FROM AUTHOR]

Previous theoretical investigations of the reactions between an OH radical and a nucleobase have stated the most important pathways to be the C5-C6 addition for pyrimidines and the C8 addition for purines. Furthermore, the abstraction of a methyl hydrogen from thymine has also been proven an important pathway. The conclusions were based solely on gas-phase calculations and harmonic vibrational frequencies. In this paper, we supplement the calculations by applying solvent corrections through the polarizable continuum model (PCM) solvent model and applying anharmonicity in order to determine the importance of anharmonicity and solvent effects. Density functional theory (DFT) at the  ω B97-D/6-311++G(2df,2pd) level with the Eckart tunneling correction is used. The total reaction rate constants are found to be 1.48  × 10 − 13  cm3 molecules−1s−1 for adenine, 1.02  × 10 − 11  cm3 molecules−1s−1 for guanine, 5.52  × 10 − 13  cm3 molecules−1s−1 for thymine, 1.47  × 10 − 13  cm3 molecules−1s−1 for cytosine and 7.59  × 10 − 14  cm3 molecules−1s−1 for uracil. These rates are found to be approximately two orders of magnitude larger than experimental values. We find that the tendencies observed for preferred pathways for reactions calculated in a solvent are comparable to the preferred pathways for reactions calculated in gas phase. We conclude that applying a solvent has a larger impact on more parameters compared to the inclusion of anharmonicity. For some reactions the inclusion of anharmonicity has no effect, whereas for others it does impact the energetics. [ABSTRACT FROM AUTHOR]

The experimental and theoretical determination of the mean excitation energy, I(0), and the stopping power, S(v), of a material is of great interest in particle and material physics and radiation therapy. For calculations of I(0), the complete set of electronic transitions in a given basis set is required, effectively limiting such calculations to systems with a small number of electrons, even at the random-phase approximation (RPA)/time-dependent Hartree–Fock (TDHF) or time-dependent density-functional theory level. To overcome such limitations, we present here the implementation of a Lanczos algorithm adapted for the paired RPA/TDHF eigenvalue problem in the Dalton program and show that it provides good approximation of the entire RPA eigenspectra in a reduced space. We observe rapid convergence of I(0) with the number of Lanczos vectors as the algorithm favors the transitions with large contributions. In most cases, the algorithm recovers RPA I(0) values of up to 0.5% accuracy at less than a quarter of the full space size. The algorithm not only exploits the RPA paired structure to save computational resources but also preserves certain sum-over-states properties, as first demonstrated by Johnson et al. [Comput. Phys. Commun. 120, 155 (1999)]. The block Lanczos RPA solver, as presented here, thus shows promise for computing mean excitation energies for systems larger than what was computationally feasible before. [ABSTRACT FROM AUTHOR]

The performance of different polarization propagator methods, such as RPA, RPA(D), HRPA, HRPA(D), and SOPPA, have been tested against CC3 values for both static and dynamic polarizabilities. The test set consists of 14 (hetero-)aromatic medium-sized organic molecules, mostly with a high degree of symmetry. The benchmark of the methods remarkably reveals that RPA and HRPA(D) yield results comparable with the CC3 values and that they outperform SOPPA for these molecules. For a subset of the molecules, a comparison could be made to experimental values. The comparison for static polarizabilities proves that RPA and HRPA(D) as well as RPA(D) reproduce experimental values to a satisfying precision, whereas the SOPPA method compared to these three methods appears to perform only adequately. An investigation of the performance of Sadlej's polarized triple zeta basis set against Dunning's aug-cc-pVTZ basis set was also carried out. It is found that in contrast to other methods, Sadlej's basis set did not perform sufficiently compared to the larger aug-cc-pVTZ basis set for the RPA based methods. [ABSTRACT FROM AUTHOR]

The Dalton Project provides a uniform platform access to the underlying full-fledged quantum chemistry codes Dalton and LSDalton as well as the PyFraME package for automatized fragmentation and parameterization of complex molecular environments. The platform is written in Python and defines a means for library communication and interaction. Intermediate data such as integrals are exposed to the platform and made accessible to the user in the form of NumPy arrays, and the resulting data are extracted, analyzed, and visualized. Complex computational protocols that may, for instance, arise due to a need for environment fragmentation and configuration-space sampling of biochemical systems are readily assisted by the platform. The platform is designed to host additional software libraries and will serve as a hub for future modular software development efforts in the distributed Dalton community. [ABSTRACT FROM AUTHOR]

A theoretical framework for understanding molecular structures is crucial for the development of new technologies such as catalysts or solar cells. Apart from electronic excitation energies, however, only spectroscopic properties of molecules consisting of lighter elements can be computationally described at a high level of theory today since heavy elements require a relativistic framework, and thus far, most methods have only been derived in a non-relativistic framework. Important new technologies such as those mentioned above require molecules that contain heavier elements, and hence, there is a great need for the development of relativistic computational methods at a higher level of accuracy. Here, the Second-Order-Polarization-Propagator-Approximation (SOPPA), which has proven to be very successful in the non-relativistic case, is adapted to a relativistic framework. The equations for SOPPA are presented in their most general form, i.e., in a non-canonical spin–orbital basis, which can be reduced to the canonical case, and the expressions needed for a relativistic four-component SOPPA are obtained. The equations are one-index transformed, giving more compact expressions that correspond to those already available for the four-component RPA. The equations are ready for implementation in a four-component quantum chemistry program, which will allow both linear response properties and excitation energies to be calculated relativistically at the SOPPA level. [ABSTRACT FROM AUTHOR]

In this work we present a systematic, theoretical investigation of the 13C NMR chemical shifts for several mono-, di- and trisaccharides in the solid state. The chemical shifts have been calculated using density functional theory (DFT) together with the gauge including the projector augmented wave (GIPAW) method as implemented in the CASTEP program. We studied the changes in the 13C NMR chemical shifts in particular due to the formation of one or two glycosidic linkages and due to crystal water. The largest changes, up to 14 ppm, are observed between the mono- and disaccharides and typically for the glycosidic linkage atoms, but not in all cases. An analysis of the bond angles at the glycosidic linkage and the observed changes in chemical shifts displays no direct correlation between them. Somewhat smaller changes in the range of 2 to 5 ppm are observed when single crystal water molecules are close to some of the atoms. Relating the changes in the chemical shifts of the carbon atoms closest to the crystal water to the distance between them does, however, not lead to a simple relation between them. [ABSTRACT FROM AUTHOR]

With this work we first test various DFT functionals against CCSD(T) for calculation of EFGs at the position of Cd(II) in a very small model system, Cd(SCH3)2. Moreover, the available basis sets in ADF are tested in terms of basis set convergence, and the effect of including relativistic effects using the scalar relativistic and spin orbit ZORA Hamiltonians is explored. The results indicate that an error of up to around 10% on the calculated EFG may be expected using spin–orbit ZORA and the BHandHLYP functional with a locally dense basis set. Next, this method was applied to model systems of the CueR protein, aiming to interpret 111Ag-PAC spectroscopic data. Note that 111Ag decays to 111Cd on which the PAC data are recorded. Surprisingly, model systems truncated – as is often done – at the first C–C bond from the central Cd(II) are inadequate in size, and larger model systems must be employed to achieve reliable EFG calculations. The calculated EFGs agree well with experimental PAC data, and indicate that shortly after the nuclear decay the structure relaxes from linear two-coordinate AgS2 in the native protein, to a structure (or structures) where Cd(II) recruits additional ligands such as backbone carbonyl oxygens to achieve higher coordination number(s). [ABSTRACT FROM AUTHOR]

All practically possible hydrogen abstraction reactions for guanosine and uridine have been investigated through quantum chemical calculations of energy barriers and rate constants. This was done at the level of density functional theory (DFT) with the ω B97X-D functional and the 6-311++G(2df,2pd) Pople basis set. Transition state theory with the Eckart tunneling correction was used to calculate the rate constants. The results show that the reaction involving the hydrogen labelled C4' in the ribofuranose part has the largest rate constant for guanosine with the value 5.097 × 10 10 L mol − 1 s − 1 and the largest for uridine with the value 1.62 × 10 10 L mol − 1 s − 1 . Based on the results for these two nucleosides, there is a noticeable similarity between the rate constants in the ribofuranose part of the molecule, even though they are bound to two entirely different nucleobases. [ABSTRACT FROM AUTHOR]

In this work, 242 NMR spin–spin coupling constants (SSCC) in 20 molecules are calculated, either with correlated wave function methods, SOPPA and HRPA(D), or with density functional theory based on the B3LYP, BHandH, or PBE0 functionals. The calculations were carried out with and without treatment of solvation via a polarizable continuum model in both the geometry optimization step and/or the SSCC calculation, and thereby, four series of calculations were considered (the full-vacuum calculation, the full-solvent calculation, and the two cross combinations). The results were compared with experimental results measured in a solvent. With the goal of reproducing experimental values, we find that the performance of the PBE0 and BHandH SSCCs improves upon including solvation effects. On the other hand, the quality of the B3LYP SSCCs worsens with the inclusion of solvation. Solvation had almost no effect on the performance of the SOPPA and HRPA(D) calculations. We find that the PBE0-based calculations of the spin–spin coupling constants have the best agreement with the experimental data. [ABSTRACT FROM AUTHOR]

A test set of N,N,N',N'-tetrasubstituted p-phenylenediamines are experimentally explored using ESR (electron spin resonance) spectroscopy and analysed from a computational standpoint thereafter. This computational study aims to further aid structural characterisation by comparing experimental ESR hyperfine coupling constants (hfccs) with computed values calculated using ESR-optimised "J-style" basis sets (6-31G(d,p)-J, 6-31G(d,p)-J, 6-311++G(d,p)-J, pcJ-1, pcJ-2 and cc-pVTZ-J) and hybrid-DFT functionals (B3LYP, PBE0, TPSSh, ω B97XD) as well as MP2. PBE0/6-31g(d,p)-J with a polarised continuum solvation model (PCM) correlated best with the experiment, giving an R 2 value of 0.8926. A total of 98% of couplings were deemed satisfactory, with five couplings observed as outlier results, thus degrading correlation values significantly. A higher-level electronic structure method, namely MP2, was sought to improve outlier couplings, but only a minority of couples showed improvement, whilst the remaining majority of couplings were negatively degraded. [ABSTRACT FROM AUTHOR]

The complexation of MgII with adenosine 5′‐triphosphate (ATP) is omnipresent in biochemical energy conversion, but is difficult to interrogate directly. Here we use the spin‐1/2 β‐emitter 31Mg to study MgII‐ATP complexation in 1‐ethyl‐3‐methylimidazolium acetate (EMIM‐Ac) solutions using β‐radiation‐detected nuclear magnetic resonance (β‐NMR). We demonstrate that (nuclear) spin‐polarized 31Mg, following ion‐implantation from an accelerator beamline into EMIM‐Ac, binds to ATP within its radioactive lifetime before depolarizing. The evolution of the spectra with solute concentration indicates that the implanted 31Mg initially bind to the solvent acetate anions, whereafter they undergo dynamic exchange and form either a mono‐ (31Mg‐ATP) or di‐nuclear (31MgMg‐ATP) complex. The chemical shift of 31Mg‐ATP is observed up‐field of 31MgMg‐ATP, in accord with quantum chemical calculations. These observations constitute a crucial advance towards using β‐NMR to probe chemistry and biochemistry in solution. [ABSTRACT FROM AUTHOR]

Substituent effects for (super 2)J(F,F) couplings in aliphatic and olefinic CF2 moieties and (super 3)J(F, F) couplings in fluorinated derivatives of ethylene are studied using both high levels ab initio and DFT/B3LYP calculations. The J variations are compared with experimental values.

Nuclear magnetic resonance (NMR) is a spectroscopic method that can be applied to several areas. Currently, this technique is also being used as an experimental quantum simulator, where nuclear spins are employed as quantum bits or qubits. The present work is devoted to studying heavy metal complexes as possible candidates to act as qubit molecules. Nuclei such 113Cd, 199Hg, 125Te, and 77Se assembled with the most common employed nuclei in NMR-QIP implementations (1H, 13C, 19F, 29Si, and 31P) could potentially be used in heteronuclear systems for NMR-QIP implementations. Hence, aiming to contribute to the development of future scalable heteronuclear spin systems, we specially designed four complexes, based on the auspicious qubit systems proposed in our previous work, which will be explored by quantum chemical calculations of their NMR parameters and proposed as suitable qubit molecules. Chemical shifts and spin–spin coupling constants in four complexes were examined using the spin–orbit zeroth-order regular approximation (ZORA) at the density functional theory (DFT) level, as well as the relaxation parameters ( T 1 and T 2 ). Examining the required spectral properties of NMR-QIP, all the designed complexes were found to be promising candidates for qubit molecules. [ABSTRACT FROM AUTHOR]