Quantum mechanical fragment methods based on partitioning atoms or partitioning coordinates

Competition between Solvent···Solvent and Solvent···Solute Interactions in the Microhydration of the Tetrafluoroborate Anion, BF4-(H2O)n=1,2,3,4

This study systematically examines the interactions of the tetrafluoroborate anion (BF4-) with up to four water molecules (BF4-(H2O)n=1,2,3,4). Full geometry optimizations and subsequent harmonic vibrational frequency computations are performed using a variety of density functional theory (DFT) methods (B3LYP, B3LYP-D3BJ, and M06-2X) and the MP2 ab initio method with a triple-ζ correlation consistent basis set augmented with diffuse functions on all non-hydrogen atoms (cc-pVTZ for H and aug-cc-pVTZ for B, O, and F; denoted as haTZ). Optimized structures and harmonic vibrational frequencies were also obtained with the CCSD(T) ab initio method and the haTZ basis set for the mono- and dihydrate (n = 1, 2) structures. The 2-body:Many-body (2b:Mb) technique, in which CCSD(T) computations capture the 1- and 2-body contributions to the interactions and MP2 computations recover all higher-order contributions, was used to extend these demanding computations to the tri- and tetrahydrate (n = 3, 4) systems. Four, five, and eight new stationary points have been identified for the di-, tri-, and tetrahydrate systems, respectively. The global minimum of the monohydrate adopts a symmetric double ionic hydrogen bond motif with C2v symmetry and an electronic dissociation energy of 13.17 kcal mol-1 at the CCSD(T)/haTZ level of theory. This strong solvent···solute interaction, however, competes with solute···solute interactions in the lowest-energy BF4-(H2O)n=2,3,4 minima that are not seen in the other di-, tri-, or tetrahydrate minima. The latter interactions help increase the 2b:Mb dissociation energies to more than 26, 41, and 51 kcal mol-1 for n = 2, 3, and 4, respectively. Structures that form hydrogen bonds between the solvating water molecules also exhibit the largest shifts in the harmonic OH stretching frequencies for the waters of hydration. These shifts can exceed -280 cm-1 relative to an isolated H2O molecule at the 2b:Mb/haTZ level of theory.

Corrigendum: Coupled cluster theory on modern heterogeneous supercomputers

[This corrects the article DOI: 10.3389/fchem.2023.1154526.].

CrystalClear: an open, modular protocol for predicting molecular crystal growth from solution

We present a new protocol for the prediction of free energies that determine the growth of sites in molecular crystals for subsequent use in Monte Carlo simulations using tools such as CrystalGrower [Hill et al., Chemical Science, 2021, 12, 1126-1146]. Key features of the proposed approach are that it requires minimal input, namely the crystal structure and solvent only, and provides automated, rapid generation of the interaction energies. The constituent components of this protocol, namely interactions between molecules (growth units) in the crystal, solvation contributions and treatment of long-range interactions are described in detail. The power of this method is shown via prediction of crystal shapes for ibuprofen grown from ethanol, ethyl acetate, toluene and acetonitrile, adipic acid grown from water, and five polymorphs (ON, OP, Y, YT04 and R) of ROY (5-methyl-2-[(2-nitrophenyl)amino]-3-thiophenecarbonitrile), with promising results. The predicted energies may be used directly or subsequently refined against experimental data, facilitating insight into the interactions governing crystal growth, while also providing a prediction of the solubility of the material. The protocol has been implemented in standalone, open-source software made available alongside this publication.

Coupled cluster theory on modern heterogeneous supercomputers

This study examines the computational challenges in elucidating intricate chemical systems, particularly through ab-initio methodologies. This work highlights the Divide-Expand-Consolidate (DEC) approach for coupled cluster (CC) theory-a linear-scaling, massively parallel framework-as a viable solution. Detailed scrutiny of the DEC framework reveals its extensive applicability for large chemical systems, yet it also acknowledges inherent limitations. To mitigate these constraints, the cluster perturbation theory is presented as an effective remedy. Attention is then directed towards the CPS (D-3) model, explicitly derived from a CC singles parent and a doubles auxiliary excitation space, for computing excitation energies. The reviewed new algorithms for the CPS (D-3) method efficiently capitalize on multiple nodes and graphical processing units, expediting heavy tensor contractions. As a result, CPS (D-3) emerges as a scalable, rapid, and precise solution for computing molecular properties in large molecular systems, marking it an efficient contender to conventional CC models.

Predicting the structures and vibrational spectra of molecular crystals containing large molecules with the generalized energy-based fragmentation approach

The generalized energy-based fragmentation (GEBF) approach under periodic boundary conditions (PBCs) has been developed to facilitate calculations of molecular crystals containing large molecules. The PBC-GEBF approach can help predict structures and properties of molecular crystals at different theory levels by performing molecular quantum chemistry calculations on a series of non-periodic subsystems constructed from the studied systems. A more rigorous formula of the forces on translational vectors of molecular crystals was proposed and implemented, enabling more reliable predictions of crystal structures. Our benchmark results on several typical molecular crystals show that the PBC-GEBF approach could reproduce the forces on atoms and the translational vectors and the optimized crystal structures from the corresponding conventional periodic methods. The improved PBC-GEBF approach is then applied to predict the crystal structures and vibrational spectra of two molecular crystals containing large molecules. The PBC-GEBF approach can provide a satisfactory description on the crystal structure of a molecular crystal containing 312 atoms in a unit cell at density-fitting second-order Møller-Plesset perturbation theory and density functional theory (DFT) levels and the infrared vibrational spectra of another molecular crystal containing 864 atoms in a unit cell at the DFT level. The PBC-GEBF approach is expected to be a promising theoretical tool for electronic structure calculations on molecular crystals containing large molecules.

Combined fragment-based machine learning force field with classical force field and its application in the NMR calculations of macromolecules in solutions

We have developed a combined fragment-based machine learning (ML) force field and molecular mechanics (MM) force field for simulating the structures of macromolecules in solutions, and then compute its NMR chemical shifts with the generalized energy-based fragmentation (GEBF) approach at the level of density functional theory (DFT). In this work, we first construct Gaussian approximation potential based on GEBF subsystems of macromolecules for MD simulations and then a GEBF-based neural network (GEBF-NN) with deep potential model for the studied macromolecule. Then, we develop a GEBF-NN/MM force field for macromolecules in solutions by combining the GEBF-NN force field for the solute molecule and ff14SB force field for solvent molecules. Using the GEBF-NN/MM MD simulation to generate snapshot structures of solute/solvent clusters, we then perform the NMR calculations with the GEBF approach at the DFT level to calculate NMR chemical shifts of the solute molecule. Taking a heptamer of oligopyridine-dicarboxamides in chloroform solution as an example, our results show that the GEBF-NN force field is quite accurate for this heptamer by comparing with the reference DFT results. For this heptamer in chloroform solution, both the GEBF-NN/MM and classical MD simulations could lead to helical structures from the same initial extended structure. The GEBF-DFT NMR results indicate that the GEBF-NN/MM force field could lead to more accurate NMR chemical shifts on hydrogen atoms by comparing with the experimental NMR results. Therefore, the GEBF-NN/MM force field could be employed for predicting more accurate dynamical behaviors than the classical force field for complex systems in solutions.

Quantum embedding theories to simulate condensed systems on quantum computers

Quantum computers hold promise to improve the efficiency of quantum simulations of materials and to enable the investigation of systems and properties that are more complex than tractable at present on classical architectures. Here, we discuss computational frameworks to carry out electronic structure calculations of solids on noisy intermediate-scale quantum computers using embedding theories, and we give examples for a specific class of materials, that is, solid materials hosting spin defects. These are promising systems to build future quantum technologies, such as quantum computers, quantum sensors and quantum communication devices. Although quantum simulations on quantum architectures are in their infancy, promising results for realistic systems appear to be within reach.

A simple fragment-based method for van der Waals corrections over density functional theory

Modeling intermolecular noncovalent interactions between large molecules remains a challenge for the electron structure theory community due to the high cost. Fragment-based methods usually fare well in reducing the cost...

Generalized energy-based fragmentation approach for calculations of solvation energies of large systems

A generalized energy-based fragmentation (GEBF) approach has been combined with a universal solvation model based on solute electron density (SMD) to compute the solvation energies of general large systems (such as protein molecules) in solutions. In the GEBF-SMD method, the solvation energy of a target system could be combined by the corresponding solvation energies of various subsystems, each of which is embedded in the background point charges and surface charges on the surface of solute cavity at the positions of its atoms and neighbouring atoms outside of the subsystem. Our results show that the GEBF-SMD model could reproduce the conventional SMD solvation energies quite well for various proteins in solutions, and could significantly reduce the computational costs for the SMD calculations of large proteins. In addition, the GEBF-SMD approach is almost independent of the basis sets and the types of solvents (including protic, polar, and nonpolar ones). Also, the GEBF-SMD approach could reproduce the relative energies of various conformers of large systems in solutions. Therefore, the GEBF-SMD method is expected to be applicable for computing the solvation energies of a broad range of large systems.

A quantum mechanical computational method for modeling electrostatic and solvation effects of protein

An efficient computational approach for modeling protein electrostatic is developed according to static point-charge model distributions based on the linear-scaling EE-GMFCC (electrostatically embedded generalized molecular fractionation with conjugate caps) quantum mechanical (QM) method. In this approach, the Electrostatic-Potential atomic charges are obtained from ab initio calculation of protein, both polarization and charge transfer effect are taken into consideration. This approach shows a significant improvement in the description of electrostatic potential and solvation energy of proteins comparing with current popular molecular mechanics (MM) force fields. Therefore, it has gorgeous prospect in many applications, including accurate calculations of electric field or vibrational Stark spectroscopy in proteins and predicting protein-ligand binding affinity. It can also be applied in QM/MM calculations or electronic embedding method of ONIOM to provide a better electrostatic environment.

A computational investigation on the substrate preference of ten-eleven-translocation 2 (TET2)

TET proteins iteratively convert 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) in a Fe(ii)/α-ketoglutarate-dependent manner. Our previous biochemical studies revealed that TET proteins are more active on 5mC than on 5hmC and 5fC. However, the source of the substrate preference of TET proteins still remains largely elusive. Here, we investigated the substrate binding and catalytic mechanisms of oxidation reactions mediated by TET2 on different substrates through computational approaches. In accordance with previous experimental reports, our computational results suggest that TET2 can bind to different substrates with comparable binding affinities and the hydrogen abstraction step in the catalytic cycle acts as the rate-limiting step. Further structural characterization of the intermediate structures revealed that the 5-substitution groups on 5hmC and 5fC adopt an unfavorable orientation for hydrogen abstraction, which leads to a higher energy barrier for 5hmC and 5fC (compared to 5mC) and thus a lower catalytic efficiency. In summary, our mechanical insights demonstrate that substrate preference is the intrinsic property of TET proteins and our theoretical calculation results can guide further dry-lab or wet-lab studies on the catalytic mechanism of TET proteins as well as other Fe(ii)/α-ketoglutarate (KG)-dependent dioxygenases.

Explicit solvent simulations of the aqueous oxidation potential and reorganization energy for neutral molecules: gas phase, linear solvent response, and non-linear response contributions

First principles simulations were used to predict aqueous one-electron oxidation potentials (Eox) and associated half-cell reorganization energies (λaq) for aniline, phenol, methoxybenzene, imidazole, and dimethylsulfide. We employed quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations of the oxidized and reduced species in an explicit aqueous solvent, followed by EOM-IP-CCSD computations with effective fragment potentials for diabatic energy gaps of solvated clusters, and finally thermodynamic integration of the non-linear solvent response contribution using classical MD. A priori predicted Eox and λaq values exhibit mean absolute errors of 0.17 V and 0.06 eV, respectively, compared to experiment. We also disaggregate Eox into several well-defined free energy properties, including the gas phase adiabatic free energy of ionization (7.73 to 8.82 eV), the solvent-induced shift in the free energy of ionization due to linear solvent response (-2.01 to -2.73 eV), and the contribution from non-linear solvent response (-0.07 to -0.14 eV). The linear solvent response component is further apportioned into contributions from the solvent-induced shift in vertical ionization energy of the reduced species (ΔVIEaq) and the solvent-induced shift in negative vertical electron affinity of the ionized species (ΔNVEAaq). The simulated ΔVIEaq and ΔNVEAaq are found to contribute the principal sources of uncertainty in computational estimates of Eox and λaq. Trends in the magnitudes of disaggregated solvation properties are found to correlate with trends in structural and electronic features of the solute. Finally, conflicting approaches for evaluating the aqueous reorganization energy are contrasted and discussed, and concluding recommendations are given.

The successful merger of theoretical thermochemistry with fragment-based methods in quantum chemistry

CONSPECTUS: Quantum chemistry and electronic structure theory have proven to be essential tools to the experimental chemist, in terms of both a priori predictions that pave the way for designing new experiments and rationalizing experimental observations a posteriori. Translating the well-established success of electronic structure theory in obtaining the structures and energies of small chemical systems to increasingly larger molecules is an exciting and ongoing central theme of research in quantum chemistry. However, the prohibitive computational scaling of highly accurate ab initio electronic structure methods poses a fundamental challenge to this research endeavor. This scenario necessitates an indirect fragment-based approach wherein a large molecule is divided into small fragments and is subsequently reassembled to compute its energy accurately. In our quest to further reduce the computational expense associated with the fragment-based methods and overall enhance the applicability of electronic structure methods to large molecules, we realized that the broad ideas involved in a different area, theoretical thermochemistry, are transferable to the area of fragment-based methods. This Account focuses on the effective merger of these two disparate frontiers in quantum chemistry and how new concepts inspired by theoretical thermochemistry significantly reduce the total number of electronic structure calculations needed to be performed as part of a fragment-based method without any appreciable loss of accuracy. Throughout, the generalized connectivity based hierarchy (CBH), which we developed to solve a long-standing problem in theoretical thermochemistry, serves as the linchpin in this merger. The accuracy of our method is based on two strong foundations: (a) the apt utilization of systematic and sophisticated error-canceling schemes via CBH that result in an optimal cutting scheme at any given level of fragmentation and (b) the use of a less expensive second layer of electronic structure method to recover all the missing long-range interactions in the parent large molecule. Overall, the work featured here dramatically decreases the computational expense and empowers the execution of very accurate ab initio calculations (gold-standard CCSD(T)) on large molecules and thereby facilitates sophisticated electronic structure applications to a wide range of important chemical problems.

Explicit polarization: a quantum mechanical framework for developing next generation force fields

Molecular mechanical force fields have been successfully used to model condensed-phase and biological systems for a half century. By means of careful parametrization, such classical force fields can be used to provide useful interpretations of experimental findings and predictions of certain properties. Yet, there is a need to further improve computational accuracy for the quantitative prediction of biomolecular interactions and to model properties that depend on the wave functions and not just the energy terms. A new strategy called explicit polarization (X-Pol) has been developed to construct the potential energy surface and wave functions for macromolecular and liquid-phase simulations on the basis of quantum mechanics rather than only using quantum mechanical results to fit analytic force fields. In this spirit, this approach is called a quantum mechanical force field (QMFF).

X-Pol is a general fragment method for electronic structure calculations based on the partition of a condensed-phase or macromolecular system into subsystems (“fragments”) to achieve computational efficiency. Here, intrafragment energy and the mutual electronic polarization of interfragment interactions are treated explicitly using quantum mechanics. X-Pol can be used as a general, multilevel electronic structure model for macromolecular systems, and it can also serve as a new-generation force field. As a quantum chemical model, a variational many-body (VMB) expansion approach is used to systematically improve interfragment interactions, including exchange repulsion, charge delocalization, dispersion, and other correlation energies. As a quantum mechanical force field, these energy terms are approximated by empirical functions in the spirit of conventional molecular mechanics. This Account first reviews the formulation of X-Pol, in the full variationally correct version, in the faster embedded version, and with systematic many-body improvements. We discuss illustrative examples involving water clusters (which show the power of two-body corrections), ethylmethylimidazolium acetate ionic liquids (which reveal that the amount of charge transfer between anion and cation is much smaller than what has been assumed in some classical simulations), and a solvated protein in aqueous solution (which shows that the average charge distribution of carbonyl groups along the polypeptide chain depends strongly on their position in the sequence, whereas they are fixed in most classical force fields). The development of QMFFs also offers an opportunity to extend the accuracy of biochemical simulations to areas where classical force fields are often insufficient, especially in the areas of spectroscopy, reactivity, and enzyme catalysis.

Full-dimensional potentials and state couplings and multidimensional tunneling calculations for the photodissociation of phenol

Full-dimensional potentials and state couplings were developed for the photodissociation of phenol. We also present multidimensional tunneling calculations at the transition state on the shoulder of the first conical intersection.