Allosteric regulation in STAT3 interdomains is mediated by a rigid core: SH2 domain regulation by CCD in D170A variant.

Signal Transducer and Activator of Transcription 3 (STAT3) plays a crucial role in cancer development and thus is a viable target for cancer treatment. STAT3 functions as a dimer mediated by phosphorylation of the SRC-homology 2 (SH2) domain, a key target for therapeutic drugs. While great efforts have been employed towards the development of compounds that directly target the SH2 domain, no compound has yet been approved by the FDA due to a lack of specificity and pharmacologic efficacy. Studies have shown that allosteric regulation of SH2 via the coiled-coil domain (CCD) is an alternative drug design strategy. Several CCD effectors have been shown to modulate SH2 binding and affinity, and at the time of writing at least one drug candidate has entered phase I clinical trials. However, the mechanism for SH2 regulation via CCD is poorly understood. Here, we investigate structural and dynamic features of STAT3 and compare the wild type to the reduced function variant D170A in order to delineate mechanistic differences and propose allosteric pathways. Molecular dynamics simulations were employed to explore conformational space of STAT3 and the variant, followed by structural, conformation, and dynamic analysis. The trajectories explored show distinctive conformational changes in the SH2 domain for the D170A variant, indicating long range allosteric effects. Multiple analyses provide evidence for long range communication pathways between the two STAT3 domains, which seem to be mediated by a rigid core which connects the CCD and SH2 domains via the linker domain (LD) and transmits conformational changes through a network of short-range interactions. The proposed allosteric mechanism provides new insight into the understanding of intramolecular signaling in STAT3 and potential pharmaceutical control of STAT3 specificity and activity.

Theoretical Investigation of the X-ray Stark Effect in Small Molecules.

We have studied the Stark effect in the soft x-ray region for various small molecules by calculating the field-dependent x-ray absorption spectra. This effect is explained in terms of the response of molecular orbitals (core and valence), the molecular dipole moment, and the molecular geometry to the applied electric field. A number of consistent trends are observed linking the computed shifts in absorption energies and intensities with specific features of the molecular electronic structure. We find that both the virtual molecular orbitals (valence and/or Rydberg) as well as the core orbitals contribute to observed trends in a complementary fashion. This initial study highlights the potential impact of x-ray Stark spectroscopy as a tool to study electronic structure and environmental perturbations at a submolecular scale.

Ab Initio Investigation of Intramolecular Charge Transfer States in DMABN by Calculation of Excited State X-ray Absorption Spectra.

Dual fluorescence in 4-(dimethylamino)benzonitrile (DMABN) and its derivatives in polar solvents has been studied extensively for the past several decades. An intramolecular charge transfer (ICT) minimum on the excited state potential energy surface, in addition to the localized low-energy (LE) minimum, has been proposed as a mechanism for this dual fluorescence, with large geometric relaxation and molecular orbital reorganization a key feature of the ICT pathway. Herein, we have used both equation-of-motion coupled-cluster with single and double excitations (EOM-CCSD) and time-dependent density functional (TDDFT) methods to investigate the landscape of excited state potential energy surfaces across a number of geometric conformations proposed as ICT structures. In order to correlate these geometries and valence excited states in terms of potential experimental observables, we have calculated the nitrogen K-edge ground and excited state absorption spectra for each of the predicted "signpost" structures and identified several key spectral features that could be used to interpret a future time-resolved X-ray absorption experiment.

A critical analysis of least-squares tensor hypercontraction applied to MP3.

The least-squares tensor hypercontraction (LS-THC) approach is a promising method of reducing the high polynomial scaling of wavefunction methods, for example, those based on many-body perturbation theory or coupled cluster. Here, we focus on LS-THC-MP3 and identify four variants with differing errors and efficiency characteristics. The performance of LS-THC-MP3 is analyzed for regular test systems with up to 40 first-row atoms. We also analyze the size-extensivity/size-consistency and grid- and basis set dependence of LS-THC-MP3. Overall, the errors observed are favorably small in comparison with standard density fitting, and a more streamlined method of generating grids via pruning is suggested. A practical crossover (the point at which LS-THC-MP3 is cheaper than the canonical method) is achieved around 240 correlated electrons. Despite several drawbacks of LS-THC that have been identified: an initial non-linearity of error when increasing system size, poor description of angular correlation, and a potentially large increase in error with the basis set size, the results show that LS-THC has significant potential for practical application to MP3 and other wavefunction methods.

Transition-potential coupled cluster.

The problem of orbital relaxation in computational core-hole spectroscopies, including x-ray absorption and x-ray photoionization, has long plagued linear response approaches, including equation-of-motion coupled cluster with singles and doubles (EOM-CCSD). Instead of addressing this problem by including additional electron correlation, we propose an explicit treatment of orbital relaxation via the use of "transition potential" reference orbitals, leading to a transition-potential coupled cluster (TP-CC) family of methods. One member of this family, in particular, TP-CCSD(12), is found to essentially eliminate the orbital relaxation error and achieve the same level of accuracy for the core-hole spectra as is typically expected of EOM-CCSD in the valence region. These results show that very accurate x-ray absorption spectra for molecules with first-row atoms can be computed at a cost essentially the same as that for EOM-CCSD.

How accurate are EOM-CC4 vertical excitation energies?

We report the first investigation of the performance of EOM-CC4-an approximate equation-of-motion coupled-cluster model, which includes iterative quadruple excitations-for vertical excitation energies in molecular systems. By considering a set of 28 excited states in 10 small molecules for which we have computed CC with singles, doubles, triples, quadruples, and pentuples and full configuration interaction reference energies, we show that, in the case of excited states with a dominant contribution from the single excitations, CC4 yields excitation energies with sub-kJ mol-1 accuracy (i.e., error below 0.01 eV), in very close agreement with its more expensive CC with singles, doubles, triples, and quadruples parent. Therefore, if one aims at high accuracy, CC4 stands as a highly competitive approximate method to model molecular excited states, with a significant improvement over both CC3 and CC with singles, doubles, and triples. Our results also evidence that, although the same qualitative conclusions hold, one cannot reach the same level of accuracy for transitions with a dominant contribution from the double excitations.

Quantum Chemistry Common Driver and Databases (QCDB) and Quantum Chemistry Engine (QCEngine): Automation and interoperability among computational chemistry programs.

Community efforts in the computational molecular sciences (CMS) are evolving toward modular, open, and interoperable interfaces that work with existing community codes to provide more functionality and composability than could be achieved with a single program. The Quantum Chemistry Common Driver and Databases (QCDB) project provides such capability through an application programming interface (API) that facilitates interoperability across multiple quantum chemistry software packages. In tandem with the Molecular Sciences Software Institute and their Quantum Chemistry Archive ecosystem, the unique functionalities of several CMS programs are integrated, including CFOUR, GAMESS, NWChem, OpenMM, Psi4, Qcore, TeraChem, and Turbomole, to provide common computational functions, i.e., energy, gradient, and Hessian computations as well as molecular properties such as atomic charges and vibrational frequency analysis. Both standard users and power users benefit from adopting these APIs as they lower the language barrier of input styles and enable a standard layout of variables and data. These designs allow end-to-end interoperable programming of complex computations and provide best practices options by default.

Coupled-cluster techniques for computational chemistry: The CFOUR program package.

An up-to-date overview of the CFOUR program system is given. After providing a brief outline of the evolution of the program since its inception in 1989, a comprehensive presentation is given of its well-known capabilities for high-level coupled-cluster theory and its application to molecular properties. Subsequent to this generally well-known background information, much of the remaining content focuses on lesser-known capabilities of CFOUR, most of which have become available to the public only recently or will become available in the near future. Each of these new features is illustrated by a representative example, with additional discussion targeted to educating users as to classes of applications that are now enabled by these capabilities. Finally, some speculation about future directions is given, and the mode of distribution and support for CFOUR are outlined.

Fourth-order vibrational perturbation theory with the Watson Hamiltonian: Report of working equations and preliminary results.

A derivation of fourth-order vibrational perturbation theory (VPT4) based on the Watson Hamiltonian in dimensionless rectilinear normal coordinates is presented. Terms that are linear and cubic in the (nk + 12 ), with nk being the zeroth-order harmonic oscillator quantum numbers, appear in fourth order and extend the much simpler second-order vibrational perturbation theory model. The rather involved expressions for the fourth-order terms are derived with Rayleigh-Schrödinger perturbation theory, the process of verifying their correctness is described, and a computer code to generate the VPT4 constants from the potential energy surface derivatives is provided. The paper concludes with numerical examples featuring the H2O, Si2C, and cyclic-C3H2 molecules.

A new approach to approximate equation-of-motion coupled cluster with triple excitations.

Accurate methods for excited, ionized, and electron-attached states are critical to the study of many chemical species such as reactive intermediates, radicals, and ionized systems. The equation-of-motion coupled cluster singles, doubles, and triples (EOM-CCSDT) family of methods is very accurate (roughly similar in accuracy as for CCSDT calculations of the ground state), but the computational cost scales iteratively as the eighth power of the system size. Many approximations already exist, although most either correct only the excited state or require an iterative 𝒪(n7) procedure which can also be prohibitively expensive. In this paper, new methods, termed EOM-CCSD(T)(a) and EOM-CCSD(T)(a)*, are proposed which correct both the ground and excited states based on a shared effective Hamiltonian, and the latter of which includes only non-iterative corrections to both the CCSD and EOM-CCSD energies. These methods are found to significantly improve the description of excited and ionized potential energy surfaces, equilibrium geometries, and harmonic frequencies; the accuracy is very close to that of full EOM-CCSDT.

Communication: An accurate calculation of the S1 C2H2 cis-trans isomerization barrier height.

A high level ab initio calculation of the cis-trans isomerization barrier height in the first excited singlet electronic state of acetylene is found to agree very well with a recent experimental determination.

Assessment of the accuracy of coupled cluster perturbation theory for open-shell systems. I. Triples expansions.

The accuracy at which total energies of open-shell atoms and organic radicals may be calculated is assessed for selected coupled cluster perturbative triples expansions, all of which augment the coupled cluster singles and doubles (CCSD) energy by a non-iterative correction for the effect of triple excitations. Namely, the second- through sixth-order models of the recently proposed CCSD(T-n) triples series [J. J. Eriksen et al., J. Chem. Phys. 140, 064108 (2014)] are compared to the acclaimed CCSD(T) model for both unrestricted as well as restricted open-shell Hartree-Fock (UHF/ROHF) reference determinants. By comparing UHF- and ROHF-based statistical results for a test set of 18 modest-sized open-shell species with comparable RHF-based results, no behavioral differences are observed for the higher-order models of the CCSD(T-n) series in their correlated descriptions of closed- and open-shell species. In particular, we find that the convergence rate throughout the series towards the coupled cluster singles, doubles, and triples (CCSDT) solution is identical for the two cases. For the CCSD(T) model, on the other hand, not only its numerical consistency, but also its established, yet fortuitous cancellation of errors breaks down in the transition from closed- to open-shell systems. The higher-order CCSD(T-n) models (orders n > 3) thus offer a consistent and significant improvement in accuracy relative to CCSDT over the CCSD(T) model, equally for RHF, UHF, and ROHF reference determinants, albeit at an increased computational cost.

Assessment of the accuracy of coupled cluster perturbation theory for open-shell systems. II. Quadruples expansions.

We extend our assessment of the potential of perturbative coupled cluster (CC) expansions for a test set of open-shell atoms and organic radicals to the description of quadruple excitations. Namely, the second- through sixth-order models of the recently proposed CCSDT(Q-n) quadruples series [J. J. Eriksen et al., J. Chem. Phys. 140, 064108 (2014)] are compared to the prominent CCSDT(Q) and ΛCCSDT(Q) models. From a comparison of the models in terms of their recovery of total CC singles, doubles, triples, and quadruples (CCSDTQ) energies, we find that the performance of the CCSDT(Q-n) models is independent of the reference used (unrestricted or restricted (open-shell) Hartree-Fock), in contrast to the CCSDT(Q) and ΛCCSDT(Q) models, for which the accuracy is strongly dependent on the spin of the molecular ground state. By further comparing the ability of the models to recover relative CCSDTQ total atomization energies, the discrepancy between them is found to be even more pronounced, stressing how a balanced description of both closed- and open-shell species-as found in the CCSDT(Q-n) models-is indeed of paramount importance if any perturbative CC model is to be of chemical relevance for high-accuracy applications. In particular, the third-order CCSDT(Q-3) model is found to offer an encouraging alternative to the existing choices of quadruples models used in modern computational thermochemistry, since the model is still only of moderate cost, albeit markedly more costly than, e.g., the CCSDT(Q) and ΛCCSDT(Q) models.

Convergence of coupled cluster perturbation theory.

The convergence of a recently proposed coupled cluster (CC) family of perturbation series [J. J. Eriksen et al., J. Chem. Phys. 140, 064108 (2014)], in which the energetic difference between two CC models-a low-level parent and a high-level target model-is expanded in orders of the Møller-Plesset (MP) fluctuation potential, is investigated for four prototypical closed-shell systems (Ne, singlet CH2, distorted HF, and F-) in standard and augmented basis sets. In these investigations, energy corrections of the various series have been calculated to high orders and their convergence radii have been determined by probing for possible front- and back-door intruder states, the existence of which would make the series divergent. In summary, we conclude how it is primarily the choice of the target state, and not the choice of the parent state, which ultimately governs the convergence behavior of a given series. For example, restricting the target state to, say, triple or quadruple excitations might remove intruders present in series which target the full configuration interaction limit, such as the standard MP series. Furthermore, we find that whereas a CC perturbation series might converge within standard correlation consistent basis sets, it may start to diverge whenever these become augmented by diffuse functions, similar to the MP case. However, unlike for the MP case, such potential divergences are not found to invalidate the practical use of the low-order corrections of the CC perturbation series.

A view on coupled cluster perturbation theory using a bivariational Lagrangian formulation.

We consider two distinct coupled cluster (CC) perturbation series that both expand the difference between the energies of the CCSD (CC with single and double excitations) and CCSDT (CC with single, double, and triple excitations) models in orders of the Møller-Plesset fluctuation potential. We initially introduce the E-CCSD(T-n) series, in which the CCSD amplitude equations are satisfied at the expansion point, and compare it to the recently developed CCSD(T-n) series [J. J. Eriksen et al., J. Chem. Phys. 140, 064108 (2014)], in which not only the CCSD amplitude, but also the CCSD multiplier equations are satisfied at the expansion point. The computational scaling is similar for the two series, and both are term-wise size extensive with a formal convergence towards the CCSDT target energy. However, the two series are different, and the CCSD(T-n) series is found to exhibit a more rapid convergence up through the series, which we trace back to the fact that more information at the expansion point is utilized than for the E-CCSD(T-n) series. The present analysis can be generalized to any perturbation expansion representing the difference between a parent CC model and a higher-level target CC model. In general, we demonstrate that, whenever the parent parameters depend upon the perturbation operator, a perturbation expansion of the CC energy (where only parent amplitudes are used) differs from a perturbation expansion of the CC Lagrangian (where both parent amplitudes and parent multipliers are used). For the latter case, the bivariational Lagrangian formulation becomes more than a convenient mathematical tool, since it facilitates a different and faster convergent perturbation series than the simpler energy-based expansion.

Stabilization of the Simplest Criegee Intermediate from the Reaction between Ozone and Ethylene: A High-Level Quantum Chemical and Kinetic Analysis of Ozonolysis.

The fraction of the collisionally stabilized Criegee species CH2OO produced from the ozonolysis of ethylene is calculated using a two-dimensional (E, J)-grained master equation technique and semiclassical transition-state theory based on the potential energy surface obtained from high-accuracy quantum chemical calculations. Our calculated yield of 42 ± 6% for the stabilized CH2OO agrees well, within experimental error, with available (indirect) experimental results. Inclusion of angular momentum in the master equation is found to play an essential role in bringing the theoretical results into agreement with the experiment. Additionally, yields of HO and HO2 radical products are predicted to be 13 ± 6% and 17 ± 6%, respectively. In the kinetic simulation, the HO radical product is produced mostly from the stepwise decomposition mechanism of primary ozonide rather than from dissociation of hot CH2OO.

Accelerating the convergence of higher-order coupled cluster methods.

The problem of the generally inferior convergence behavior of higher-order coupled cluster methods, such as CCSDT and CCSDTQ, compared to CCSD is analyzed in terms of Møller-Plesset perturbation theory. A new structure for the CCSDT and CCSDTQ equations (and various approximations of these) is proposed which reorders contributions between the various cluster amplitudes and emphasizes lower-order corrections to the energy at each iteration. Numerical testing of the proposed method compared to the widely used direct inversion in the iterative subspace convergence acceleration technique shows significant improvement in the rate of convergence and total time-to-solution, especially for methods including quadruple excitations.

Non-orthogonal spin-adaptation of coupled cluster methods: A new implementation of methods including quadruple excitations.

The theory of non-orthogonal spin-adaptation for closed-shell molecular systems is applied to coupled cluster methods with quadruple excitations (CCSDTQ). Calculations at this level of detail are of critical importance in describing the properties of molecular systems to an accuracy which can meet or exceed modern experimental techniques. Such calculations are of significant (and growing) importance in such fields as thermodynamics, kinetics, and atomic and molecular spectroscopies. With respect to the implementation of CCSDTQ and related methods, we show that there are significant advantages to non-orthogonal spin-adaption with respect to simplification and factorization of the working equations and to creating an efficient implementation. The resulting algorithm is implemented in the CFOUR program suite for CCSDT, CCSDTQ, and various approximate methods (CCSD(T), CC3, CCSDT-n, and CCSDT(Q)).

Communication: The performance of non-iterative coupled cluster quadruples models.

We compare the numerical performance of various non-iterative coupled cluster (CC) quadruples models. The results collectively show how approaches that attempt to correct the CC singles and doubles energy for the combined effect of triple and quadruple excitations all fail at recovering the correlation energy of the full CC singles, doubles, triples, and quadruples (CCSDTQ) model to within sufficient accuracy. Such a level of accuracy is only achieved by models that make corrections to the full CC singles, doubles, and triples (CCSDT) energy for the isolated effect of quadruple excitations of which the CCSDT(Q-3) and CCSDT(Q-4) models of the Lagrangian-based CCSDT(Q-n) perturbation series are found to outperform alternative models that add either of the established [Q] and (Q) corrections to the CCSDT energy.

Heavy atom vibrational modes and low-energy vibrational autodetachment in nitromethane anions.

We report infrared spectra of nitromethane anion, CH3NO2 (-), in the region 700-2150 cm(-1), obtained by Ar predissociation spectroscopy and electron detachment spectroscopy. The data are interpreted in the framework of second-order vibrational perturbation theory based on coupled-cluster electronic structure calculations. The modes in the spectroscopic region studied here are mainly based on vibrations involving the heavier atoms; this work complements earlier studies on nitromethane anion that focused on the CH stretching region of the spectrum. Electron detachment begins at photon energies far below the adiabatic electron affinity due to thermal population of excited vibrational states.