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A summary of the technical advances that are incorporated in the fourth major release of the Q-Chem quantum chemistry program is provided, covering approximately the last seven years. These include developments in density functional theory methods and algorithms, nuclear magnetic resonance (NMR) property evaluation, coupled cluster and perturbation theories, methods for electronically excited and open-shell species, tools for treating extended environments, algorithms for walking on potential surfaces, analysis tools, energy and electron transfer modelling, parallel computing capabilities, and graphical user interfaces. In addition, a selection of example case studies that illustrate these capabilities is given. These include extensive benchmarks of the comparative accuracy of modern density functionals for bonded and non-bonded interactions, tests of attenuated second order Møller-Plesset (MP2) methods for intermolecular interactions, a variety of parallel performance benchmarks, and tests of the accuracy of implicit solvation models. Some specific chemical examples include calculations on the strongly correlated Cr2 dimer, exploring zeolite-catalysed ethane dehydrogenation, energy decomposition analysis of a charged ter-molecular complex arising from glycerol photoionisation, and natural transition orbitals for a Frenkel exciton state in a nine-unit model of a self-assembling nanotube.

An atomic-orbital reformulation of the Laplace-transformed scaled opposite-spin (SOS) coupled cluster singles and doubles (CC2) model within the resolution of the identity (RI) approximation (SOS-RI-CC2) is presented that extends its applicability to molecules with several hundreds of atoms and triple-zeta basis sets. We exploit sparse linear algebra and an attenuated Coulomb metric to decrease the disk space demands and the computational efforts. In this way, an effective sub-quadratic computational scaling is achieved with our ω-SOS-CDD-RI-CC2 model. Moreover, Cholesky decomposition of the ground-state one-electron density matrix reduces the prefactor, allowing for an early crossover with the molecular orbital formulation. The accuracy and performance of the presented method are investigated for various molecular systems. [ABSTRACT FROM AUTHOR]

Variants in genes encoding core components of the spliceosomes are associated with craniofacial syndromes, collectively called craniofacial spliceosomopathies. SNRPE encodes a core component of pre‐mRNA processing U‐rich small nuclear ribonuclear proteins (UsnRNPs). Heterozygous variants in SNRPE have been reported in six families with isolated hypotrichosis simplex in addition to one case of isolated non syndromic congenital microcephaly. Here, we report a patient with a novel blended phenotype of microcephaly and congenital atrichia with multiple congenital anomalies due to a de novo intronic SNRPE deletion, c.82‐28_82‐16del, which results in exon skipping. As discussed within, this phenotype, which we propose be named SNRPE‐related syndromic microcephaly and hypotrichosis, overlaps other craniofacial splicesosomopathies. [ABSTRACT FROM AUTHOR]

We present a low-prefactor, cubically scaling scaled-opposite-spin second-order M0ller-Plesset perturbation theory (SOS-MP2) method which is highly suitable for massively parallel architectures like graphics processing units (GPU). The scaling is reduced from 0 ( N5 ) to 0 ( N³ ) by a reformulation of the MP2-expression in the atomic orbital basis via Laplace transformation and the resolution-ofthe- identity (RI) approximation of the integrals in combination with efficient sparse algebra for the 3-center integral transformation. In contrast to previous works that employ GPUs for post Hartree- Fock calculations, we do not simply employ GPU-based linear algebra libraries to accelerate the conventional algorithm. Instead, our reformulation allows to replace the rate-determining contraction step with a modified J-engine algorithm, that has been proven to be highly efficient on GPUs. Thus, our SOS-MP2 scheme enables us to treat large molecular systems in an accurate and efficient manner on a single GPU-server. [ABSTRACT FROM AUTHOR]

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In this work, we present a novel method to directly calculate targeted electronic excited states within a self-consistent field calculation based on constrained density functional theory (cDFT). The constraint is constructed from the static occupied-occupied and virtual-virtual parts of the excited state difference density from (simplified) linear-response time-dependent density functional theory calculations (LR-TDDFT). Our new method shows a stable convergence behavior, provides an accurate excited state density adhering to the Aufbau principle, and can be solved within a restricted SCF for singlet excitations to avoid spin contamination. This also allows the straightforward application of post-SCF electron-correlation methods like MP2 or direct RPA methods. We present the details of our constraint-based orbital-optimized excited state method (COOX) and compare it to similar schemes. The accuracy of excitation energies will be analyzed for a benchmark of systems, while the quality of the resulting excited state densities is investigated by evaluating excited state nuclear forces and excited state structure optimizations. We also investigate the performance of the proposed COOX method for long-range charge transfer excitations and conical intersections with the ground-state.

Unlocking the full potential of Lewis acid catalysis for photochemical transformations requires a comprehensive understanding of the ultrafast dynamics of substrate-Lewis acid complexes. In a previous article [Peschel et al., Angew. Chem. Int. Ed. , 2021, 60 , 10155], time-resolved spectroscopy supported by static calculations revealed that the Lewis acid remains attached during the relaxation of the model complex cyclohexenone-BF 3 . In contrast to the experimental observation, surface-hopping dynamics in the gas phase predicted ultrafast heterolytic dissociation. We attributed the discrepancy to missing solvent interactions. Thus, in this work, we present an interface between the SHARC and FermiONs++ program packages, which enables us to investigate the ultrafast dynamics of cyclohexenone-BF 3 in an explicit solvent environment. Our simulations demonstrate that the solvent prevents the dissociation of the complex, leading to an intriguing dissociation-reassociation mechanism. Comparing the dynamics with and without triplet states highlights their role in the relaxation process and shows that the Lewis acid inhibits intersystem crossing. These findings provide a clear picture of the relaxation process, which may aid in designing future Lewis acid catalysts for photochemical applications. They underscore that an explicit solvent model is required to describe relaxation processes in weakly bound states, as energy transfer to the solvent is crucial for the system to reach its minimum geometries.

Water-mediated proton transfer reactions are central for catalytic processes in a wide range of biochemical systems, ranging from biological energy conversion to chemical transformations in the metabolism. Yet, the accurate computational treatment of such complex biochemical reactions is highly challenging and requires the application of multiscale methods, in particular hybrid quantum/classical (QM/MM) approaches combined with free energy simulations. Here, we combine the unique exploration power of new advanced sampling methods with density functional theory (DFT)-based QM/MM free energy methods for multiscale simulations of long-range protonation dynamics in biological systems. In this regard, we show that combining multiple walkers/well-tempered metadynamics with an extended system adaptive biasing force method (MWE) provides a powerful approach for exploration of water-mediated proton transfer reactions in complex biochemical systems. We compare and combine the MWE method also with QM/MM umbrella sampling and explore the sampling of the free energy landscape with both geometric (linear combination of proton transfer distances) and physical (center of excess charge) reaction coordinates and show how these affect the convergence of the potential of mean force (PMF) and the activation free energy. We find that the QM/MM-MWE method can efficiently explore both direct and water-mediated proton transfer pathways together with forward and reverse hole transfer mechanisms in the highly complex proton channel of respiratory Complex I, while the QM/MM-US approach shows a systematic convergence of selected long-range proton transfer pathways. In this regard, we show that the PMF along multiple proton transfer pathways is recovered by combining the strengths of both approaches in a QM/MM-MWE/focused US (FUS) scheme and reveals new mechanistic insight into the proton transfer principles of Complex I. Our findings provide a promising basis for the quantitative multiscale simulations of long-range proton transfer reactions in biological systems.