Reaction Networks Resemble Low-Dimensional Regular Lattices.

The computational exploration, manipulation, and design of complex chemical reactions face fundamental challenges related to the high-dimensional nature of potential energy surfaces (PESs) that govern reactivity. Accurately modeling complex reactions is crucial for understanding the chemical processes involved in, for example, organocatalysis, autocatalytic cycles, and one-pot molecular assembly. Our prior research demonstrated that discretizing PESs using heuristics based on bond breaking and bond formation produces a reaction network representation with a low-dimensional structure (metric space).

Optical study of Te ring clusters: comparison with density functional theory and a step towards materials design using nanoporous zeolite space.

The Te ring molecule (cluster) is poorly investigated due to the lack of experimental data. Here, we report an experimental and theoretical study of a regular array of oriented Te rings formed in the ∼1.14 nm diameter cavities of zeolite LTA, which are arranged in a cubic lattice with a spacing of ∼1.

Natural determinant reference functional theory.

The natural determinant reference (NDR) or principal natural determinant is the Slater determinant comprised of the N most strongly occupied natural orbitals of an N-electron state of interest. Unlike the Kohn-Sham (KS) determinant, which yields the exact ground-state density, the NDR only yields the best idempotent approximation to the interacting one-particle reduced density matrix, but it is well-defined in common atom-centered basis sets and is representation-invariant. We show that the under-determination problem of prior attempts to define a ground-state energy functional of the NDR is overcome in a grand-canonical ensemble framework at the zero-temperature limit.

A DFT perspective on organometallic lanthanide chemistry.

Computational studies of the coordination chemistry and bonding of lanthanides have grown in recent decades as the need for understanding the distinct physical, optical, and magnetic properties of these compounds increased. Density functional theory (DFT) methods offer a favorable balance of computational cost and accuracy in lanthanide chemistry and have helped to advance the discovery of novel oxidation states and electronic configurations. This article examines the scope and limitations of DFT in interpreting structural and spectroscopic data of low-valent lanthanide complexes, elucidating periodic trends, and predicting their properties and reactivity, presented through selected examples.

TURBOMOLE: Today and Tomorrow.

TURBOMOLE is a highly optimized software suite for large-scale quantum-chemical and materials science simulations of molecules, clusters, extended systems, and periodic solids. TURBOMOLE uses Gaussian basis sets and has been designed with robust and fast quantum-chemical applications in mind, ranging from homogeneous and heterogeneous catalysis to inorganic and organic chemistry and various types of spectroscopy, light-matter interactions, and biochemistry. This Perspective briefly surveys TURBOMOLE's functionality and highlights recent developments that have taken place between 2020 and 2023, comprising new electronic structure methods for molecules and solids, previously unavailable molecular properties, embedding, and molecular dynamics approaches.

Constructing the Mechanism of Dinoflagellate Luciferin Bioluminescence Using Computation.

Dinoflagellate luciferin bioluminescence is unique since it does not rely on decarboxylation but is poorly understood compared to that of firefly, bacteria, and coelenterata luciferins. Here we computationally investigate possible protonation states, stereoisomers, a chemical mechanism, and the dynamics of the bioluminescence intermediate that is responsible for chemiexcitation. Using semiempirical dynamics, time-dependent density functional theory static calculations, and a correlation diagram, we find that the intermediate's functional group that is likely responsible for chemiexcitation is a 4-member ring, a dioxetanol, that undergoes [2π + 2π] cycloreversion and the biolumiphore is the cleaved structure.

Statistics and Bias-Free Sampling of Reaction Mechanisms from Reaction Network Models.

Selection bias is inevitable in manually curated computational reaction databases but can have a significant impact on generalizability of quantum chemical methods and machine learning models derived from these data sets. Here, we propose quasireaction subgraphs as a discrete, graph-based representation of reaction mechanisms that has a well-defined associated probability space and admits a similarity function using graph kernels. Quasireaction subgraphs are thus well suited for constructing representative or diverse data sets of reactions.

Implementation of the self-consistent phonons method with ab initio potentials (AI-SCP).

The self-consistent phonon (SCP) method allows one to include anharmonic effects when treating a many-body quantum system at thermal equilibrium. The system is then described by an effective temperature-dependent harmonic Hamiltonian, which can be used to estimate its various dynamic and static properties. In this paper, we combine SCP with ab initio (AI) potential energy evaluation in which case the numerical bottleneck of AI-SCP is the evaluation of Gaussian averages of the AI potential energy and its derivatives.

Enzyme Substrate Prediction from Three-Dimensional Feature Representations Using Space-Filling Curves.

Compact and interpretable structural feature representations are required for accurately predicting properties and function of proteins. In this work, we construct and evaluate three-dimensional feature representations of protein structures based on space-filling curves (SFCs). We focus on the problem of enzyme substrate prediction, using two ubiquitous enzyme families as case studies: the short-chain dehydrogenase/reductases (SDRs) and the -adenosylmethionine-dependent methyltransferases (SAM-MTases).

Libkrylov: A modular open-source software library for extremely large on-the-fly matrix computations.

We present the design and implementation of libkrylov, an open-source library for solving matrix-free eigenvalue, linear, and shifted linear equations using Krylov subspace methods. The primary objectives of libkrylov are flexible API design and modular structure, which enables integration with specialized matrix-vector evaluation "engines." Libkrylov features pluggable preconditioning, orthonormalization, and tunable convergence control.

Solid-State End-On to Side-On Isomerization of (N═N) in {[(RN)Nd]N} (R = SiMe) Connects In Situ Ln(NR)/K and Isolated [Ln(NR)] Dinitrogen Reduction.

Examination of the reduction chemistry of Nd(NR) (R = SiMe) under N has provided connections between the in situ Ln(III)-based Ln(NR)/K reductions of N that form side-on bound neutral (N=N) complexes, [(RN)(THF)Ln][μ-η:η-N], and the Ln(II)-based [Ln(NR)] reductions by Sc, Gd, and Tb that form end-on bound (N=N) complexes, {[(RN)Ln][μ-η:η-N]}, which are dianions. The reduction of Nd(NR) by KC under dinitrogen in EtO in the presence of 18-crown-6 (18-c-6) forms dark yellow solutions of [K(18-c-6)]{[(RN)Nd]N} at low temperatures that become green as they warm up to -35 °C in a glovebox freezer. Green crystals obtained from the solution turn yellow-brown when cooled below -100 °C, and the yellow-brown compound has an end-on Nd(μ-η:η-N) structure.

Property-optimized Gaussian basis sets for lanthanides.

Property-optimized Gaussian basis sets of split-valence, triple-zeta valence, and quadruple-zeta valence quality are developed for the lanthanides Ce-Lu for use with small-core relativistic effective core potentials. They are constructed in a systematic fashion by augmenting def2 orbital basis sets with diffuse basis functions and minimizing negative static isotropic polarizabilities of lanthanide atoms with respect to basis set exponents within the unrestricted Hartree-Fock method. The basis set quality is assessed using a test set of 70 molecules containing the lanthanides in their common oxidation states and f electron occupations.

TURBOMOLE: Modular program suite for ab initio quantum-chemical and condensed-matter simulations.

TURBOMOLE is a collaborative, multi-national software development project aiming to provide highly efficient and stable computational tools for quantum chemical simulations of molecules, clusters, periodic systems, and solutions. The TURBOMOLE software suite is optimized for widely available, inexpensive, and resource-efficient hardware such as multi-core workstations and small computer clusters. TURBOMOLE specializes in electronic structure methods with outstanding accuracy-cost ratio, such as density functional theory including local hybrids and the random phase approximation (RPA), GW-Bethe-Salpeter methods, second-order Møller-Plesset theory, and explicitly correlated coupled-cluster methods.

Predicting Feasible Organic Reaction Pathways Using Heuristically Aided Quantum Chemistry.

Studying organic reaction mechanisms using quantum chemical methods requires from the researcher an extensive knowledge of both organic chemistry and first-principles computation. The need for empirical knowledge arises because any reasonably complete exploration of the potential energy surfaces (PES) of organic reactions is computationally prohibitive. We have previously introduced the heuristically-aided quantum chemistry (HAQC) approach to modeling complex chemical reactions, which abstracts the empirical knowledge in terms of chemical heuristics-simple rules guiding the PES exploration-and combines them with structure optimizations using quantum chemical methods.

Charge Transport through Self-Assembled Monolayers of Monoterpenoids.

The nature of the processes at the origin of life that selected specific classes of molecules for broad incorporation into cells is controversial. Among those classes selected were polyisoprenoids and their derivatives. This paper tests the hypothesis that polyisoprenoids were early contributors to membranes in part because they (or their derivatives) could facilitate charge transport by quantum tunneling.

Reaction Networks and the Metric Structure of Chemical Space(s).

In this paper, we develop a formal definition of chemical space as a discrete metric space of molecules and analyze its properties. To this end, we utilize the shortest path metric on reaction networks to define a distance function between molecules of the same stoichiometry (number of atoms). The distance between molecules with different stoichiometries is formalized by making use of the partial ordering of stoichiometries with respect to inclusion.

Excitonics: A Set of Gates for Molecular Exciton Processing and Signaling.

Regulating energy transfer pathways through materials is a central goal of nanotechnology, as a greater degree of control is crucial for developing sensing, spectroscopy, microscopy, and computing applications. Such control necessitates a toolbox of actuation methods that can direct energy transfer based on user input. Here we introduce a proposal for a molecular exciton gate, analogous to a traditional transistor, for regulating exciton flow in chromophoric systems.

Quadratic Response Properties from TDDFT: Trials and Tribulations.

We report on the efficient turbomole implementation of quadratic response properties within the time-dependent density functional theory (TDDFT) context that includes the static and dynamic dipole hyperpolarizability, ground-to-excited-state two-photon absorption amplitudes (through a single residue) and state-to-state one-photon absorption amplitudes (through a double residue). Our implementation makes full use of arbitrary (including non-Abelian) point-group symmetry as well as permutational symmetry and enables the calculation of nonlinear properties with hybrid density functionals for molecules with hundreds of atoms and thousands of basis functions at a cost that is a fixed multiple of the cost of the corresponding linear properties. Using the PBE0 hybrid density functional, we show that excited-state absorption spectra computed within the pseudowavefunction approach contain the qualitative features of transient absorption spectra tracking excimer formation in perylene diimide dimers, two-photon absorption cross sections for a series of highly twisted fused porphyrin chains are semiquantitatively reproduced, and the computed dynamic hyperpolarizability of several calix[4]arene stereoisomers yield simulated hyper-Raleigh scattering signals consistent with experiment.

Anomalously Rapid Tunneling: Charge Transport across Self-Assembled Monolayers of Oligo(ethylene glycol).

This paper describes charge transport by tunneling across self-assembled monolayers (SAMs) of thiol-terminated derivatives of oligo(ethylene glycol) (HS(CHCHO)CH; HS(EG)CH); these SAMs are positioned between gold bottom electrodes and GaO/EGaIn top electrodes. Comparison of the attenuation factor (β of the simplified Simmons equation) across these SAMs with the corresponding value obtained with length-matched SAMs of oligophenyls (HS(Ph)H) and n-alkanethiols (HS(CH)H) demonstrates that SAMs of oligo(ethylene glycol) have values of β (β = 0.29 ± 0.

Charge Tunneling along Short Oligoglycine Chains.

This work examines charge transport (CT) through self-assembled monolayers (SAMs) of oligoglycines having an N-terminal cysteine group that anchors the molecule to a gold substrate, and demonstrate that CT is rapid (relative to SAMs of n-alkanethiolates). Comparisons of rates of charge transport-using junctions with the structure Au(TS)/SAM//Ga2O3/EGaIn (across these SAMs of oligoglycines, and across SAMs of a number of structurally and electronically related molecules) established that rates of charge tunneling along SAMs of oligoglycines are comparable to that along SAMs of oligophenyl groups (of comparable length). The mechanism of tunneling in oligoglycines is compatible with superexchange, and involves interactions among high-energy occupied orbitals in multiple, consecutive amide bonds, which may by separated by one to three methylene groups.

Uncertainty of prebiotic scenarios: the case of the non-enzymatic reverse tricarboxylic acid cycle.

We consider the hypothesis of the primordial nature of the non-enzymatic reverse tricarboxylic acid (rTCA) cycle and describe a modeling approach to quantify the uncertainty of this hypothesis due to the combinatorial aspect of the constituent chemical transformations. Our results suggest that a) rTCA cycle belongs to a degenerate optimum of auto-catalytic cycles, and b) the set of targets for investigations of the origin of the common metabolic core should be significantly extended.

Characterizing the metal-SAM interface in tunneling junctions.

This paper investigates the influence of the interface between a gold or silver metal electrode and an n-alkyl SAM (supported on that electrode) on the rate of charge transport across junctions with structure Met(Au or Ag)(TS)/A(CH2)nH//Ga2O3/EGaIn by comparing measurements of current density, J(V), for Met/AR = Au/thiolate (Au/SR), Ag/thiolate (Ag/SR), Ag/carboxylate (Ag/O2CR), and Au/acetylene (Au/C≡CR), where R is an n-alkyl group. Values of J0 and β (from the Simmons equation) were indistinguishable for these four interfaces. Since the anchoring groups, A, have large differences in their physical and electronic properties, the observation that they are indistinguishable in their influence on the injection current, J0 (V = 0.

Development of new auxiliary basis functions of the Karlsruhe segmented contracted basis sets including diffuse basis functions (def2-SVPD, def2-TZVPPD, and def2-QVPPD) for RI-MP2 and RI-CC calculations.

We report optimized auxiliary basis sets for use with the Karlsruhe segmented contracted basis sets including moderately diffuse basis functions (Rappoport and Furche, J. Chem. Phys.

Quantum chemical approach to estimating the thermodynamics of metabolic reactions.

Thermodynamics plays an increasingly important role in modeling and engineering metabolism. We present the first nonempirical computational method for estimating standard Gibbs reaction energies of metabolic reactions based on quantum chemistry, which can help fill in the gaps in the existing thermodynamic data. When applied to a test set of reactions from core metabolism, the quantum chemical approach is comparable in accuracy to group contribution methods for isomerization and group transfer reactions and for reactions not including multiply charged anions.

State-by-state investigation of destructive interference in resonance Raman spectra of neutral tyrosine and the tyrosinate anion with the simplified sum-over-states approach.

UV resonance Raman scattering is uniquely sensitive to the molecular electronic structure as well as intermolecular interactions. To better understand the relationship between electronic structure and resonance Raman cross section, we carried out combined experimental and theoretical studies of neutral tyrosine and the tyrosinate anion. We studied the Raman cross sections of four vibrational modes as a function of excitation wavelength, and we analyzed them in terms of the contributions of the individual electronic states as well as of the Albrecht A and B terms.