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The bonding structures of CO3Li3+ and CS3Li3+ are studied by means of oriented quasi-atomic orbitals (QUAOs) to assess the possibility of these molecules being planar hexacoordinated carbon (phC) systems. CH3Li and CO32- are employed as reference molecules. It is found that the introduction of Li+ ions into the molecular environment of carbonate has a greater effect on the orbital structure of the O atoms than it does on the C atom. Partial charges computed from QUAO populations imply repulsion between the positively charged C and Li atoms in CO3Li3+. Upon the transition from CO3Li3+ to CS3Li3+, the analysis reveals that the substitution of O atoms by S atoms inverts the polarity of the carbon-chalcogen σ bond. This is linked to the difference in s- and p-fractions of the QUAOs of C and S, as element electronegativities do not explain the observed polarity of the CSσ bond. Partial charges indicate that the larger electron population on the C atom in CS3Li3+ makes C-Li attraction possible. Upon comparison with the C-Li bond in methyllithium, it is found that the C-Li covalent interactions in CO3Li3+ and CS3Li3+ have about 14% and 6% of the strength of the C-Li covalent interaction in CH3Li, respectively. Consequently, it is concluded that only CS3Li3+ may be considered to be a phC system.
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The bonding structures of infinitene, the Chemical and Engineering News 2021 Molecule of the Year, is studied by means of oriented quasi-atomic orbitals (QUAOs) to assess the degree of aromaticity within the molecule. It is found that the angularity introduced into infinitene when it takes on the helical shape of the infinity symbol has a profound effect on bond order, delocalization of bonding interactions, and the aromatic character of the system. In kekulene, a planar isomer of infinitene, the bonding analysis shows fluctuations of pocketed delocalization of bonding interactions in π-sextets associated with Clar's rule. Conversely, much smaller fluctuations are observed between the adjacent rings of infinitene. The observations drawn from the quasi-atomic bonding analysis support the idea that there is aromatic character across the entire infinitene molecule, not just localized around individual rings as in kekulene.
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The anisotropic and isotropic R-8 dispersion contributions (disp8) are derived and implemented within the framework of the effective fragment potential (EFP) method formulated with imaginary frequency-dependent Cartesian polarizability tensors distributed at the centroids of the localized molecular orbitals (LMOs). Two forms of damping functions, intermolecular overlap-based and Tang-Toennies, are extended for disp8. To obtain LMO polarizability tensors centered at LMO centroids, an origin-shifting transformation is derived and implemented for the dipole-octopole polarizability tensor and the quadrupole-quadrupole polarizability tensor. The analytic gradient is derived and implemented for the isotropic disp8 contribution. Relative to the previously implemented empirical EFP disp8 energy, the isotropic disp8 component of the interaction energy improves the overall agreement of the EFP dispersion energies with the symmetry-adapted perturbation theory (SAPT) benchmarks, reducing the mean absolute errors (MAEs) and mean absolute percentage errors for most of the databases examined in this work. While the anisotropic disp8 can further enhance the accuracy of the EFP dispersion energy and yield smaller MAEs, significantly overbound dispersion energies are predicted by the anisotropic disp8 when the maximum element in the intermolecular overlap matrix is greater than 0.1, possibly due to the breakdown of the approximations made in the EFP dispersion derivation at a short range. For potential energy scan databases, the newly developed EFP dispersion model with isotropic disp8 yields the overall correct curvature and good agreement with SAPT benchmarks around equilibrium and longer but overestimates the dispersion interactions at a short range. While the overlap-based dispersion-damping functions produce better MAEs than Tang-Toennies damping functions, further improvement is needed to better screen the large attractive dispersion energies at a short range (overlap >0.1).
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A portable and performant graphics processing unit (GPU)-accelerated library for electron repulsion integral (ERI) evaluation, named LibERI, has been developed and implemented via directive-based (e.g., OpenMP and OpenACC) and standard language parallelism (e.g., Fortran DO CONCURRENT). Offloaded ERIs consist of integrals over low and high contraction s, p, and d functions using the rotated-axis and Rys quadrature methods. GPU codes are factorized based on previous developments [Pham et al., J. Chem. Theory Comput. 19(8), 2213-2221 (2023)] with two layers of integral screening and quartet presorting. In this work, the density screening is moved to the GPU to enhance the computational efficacy for large molecular systems. The L-shells in the Pople basis set are also separated into pure S and P shells to increase the ERI homogeneity and reduce atomic operations and the memory footprint. LibERI is compatible with any quantum chemistry drivers supporting the MolSSI Driver Interface. Benchmark calculations of LibERI interfaced with the GAMESS software package were carried out on various GPU architectures and molecular systems. The results show that the LibERI performance is comparable to other state-of-the-art GPU-accelerated codes (e.g., TeraChem and GMSHPC) and, in some cases, outperforms conventionally developed ERI CUDA kernels (e.g., QUICK) while fully maintaining portability.
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The new LOGKPREDICT program integrates HostDesigner molecular design software with the machine learning (ML) program Chemprop. By supplying HostDesigner with predicted log K values, LOGKPREDICT enhances the computer-aided molecular design process by ranking ligands directly by metal-ligand binding strength. Harnessing reliable experimental data from a historic National Institute of Standards and Technology (NIST) database and data from the International Union of Pure and Applied Chemistry (IUPAC), we train message passing neural net algorithms. The multi-metal NIST-based ML model has a root mean square error (RMSE) of 0.629 ± 0.044 (R2 of 0.960 ± 0.006), while two versions of lanthanide-only IUPAC-based ML models have, respectively, RMSE of 0.764 ± 0.073 (R2 of 0.976 ± 0.005) and 0.757 ± 0.071 (R2 of 0.959 ± 0.007). For relative log K predictions on an out-of-sample set of six ligands, demonstrating metal ion selectivity, the RMSE value reaches a commendably low 0.25. We showcase the use of LOGKPREDICT in identifying ligands with high selectivity for lanthanides in aqueous solutions, a finding supported by recent experimental evidence. We also predict new ligands yet to be verified experimentally. Therefore, our ML models implemented through LOGKPREDICT and interfaced with the ligand design software HostDesigner pave the way for designing new ligands with predetermined selectivity for competing metal ions in an aqueous solution.
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The bonding structures of tetrahedrane, phosphatetrahedrane, diphosphatetrahedrane and triphosphatetrahedrane are studied by employing an intrinsic quasi-atomic orbital analysis. Ethane, cyclopropane and tetrahedral P4 are employed as reference systems. The orbital analysis is paired with the computation of strain energies via isodesmic reactions. The results show that the increase in geometric strain upon transition from ethane to cyclopropane to tetrahedrane weakens the CC bonds, despite leading to shorter C-C interatomic distances. With the increase in strain, the orbitals centered on C and involved in the bonding of the cage structure are observed to have elevated p-character, and the orbital structure of C deviates from sp3 hybridization. The systematic substitution of CH groups by P atoms in the cage structure of tetrahedrane leads to stronger CC bonds, larger angles in the cage structures of the resulting phosphatetrahedranes, lower p-character in the orbitals involved in the bonding of the cages, and lower strain energies. It is found that P is more amenable to strained molecular arrangements than is C, and that the propensity of a given atom to hybridize s and p functions, or the lack thereof, has implications in the stability of molecules with strained geometries. The combination of the calculations presented here with the existing literature provides insight into the apparent propensity of tetrahedrane and P4 to 'break' their tetrahedral structures. Trends in the bonding interactions, such as bond strengths, s- and p-orbital characters and charge transfer are identified and related to the strain energy observed in each of the analyzed systems.
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The intermolecular interaction energies, including hydrogen bonds (H-bonds), of clusters of the ionic liquid ethylammonium nitrate (EAN) and 1-amino-1,2,3-triazole (1-AT) based deep eutectic propellants (DeEP) are examined. 1-AT is introduced as a neutral hydrogen bond donor (HBD) to EAN in order to form a eutectic mixture. The effective fragment potential (EFP) is used to examine the bonding interactions in the DeEP clusters. The resolution of the Identity (RI) approximated second order Møller-Plesset perturbation theory (RI-MP2) and coupled cluster theory (RI-CCSD(T)) are used to validate the EFP results. The EFP method predicts that there are significant polarization and charge transfer effects in the EAN:1-AT complexes, along with Coulombic, dispersion and exchange repulsion interactions. The EFP interaction energies are in good agreement with the RI-MP2 and RI-CCSD(T) results. The quasi-atomic orbital (QUAO) bonding and kinetic bond order (KBO) analyses are additionally used to develop a conceptual and semi-quantitative understanding of the H-bonding interactions as a function of the size of the system. The QUAO and KBO analyses suggest that the H-bonds in the examined clusters follow the characteristic hydrogen bonding three-center four electron interactions. The strongest H-bonding interactions between the (EAN)1:(1-AT)n and (EAN)2:(1-AT)n (n = 1-5) complexes are observed internally within EAN; that is, between the ethylammonium cation [EA]+ and the nitrate anion ([NO3]-). The weakest H-bonding interactions occur between [NO3]- and 1-AT. Consequently, the average strengths of the H-bonds within a given (EAN)x:(1-AT)n complex decrease as more 1-AT molecules are introduced into the EAN monomer and EAN dimer. The QUAO bonding analysis suggests that 1-AT in (EAN)x:(1-AT)n can act as both a HBD and a hydrogen bond acceptor simultaneously. It is observed that two 1-AT molecules can form H-bonds to each other. Although the KBOs that correspond to H-bonding interactions in [EA]+:1-AT, [NO3]-:1-AT and between two 1-AT molecules are weaker than the H-bonds in EAN, those weak H-bond networks with 1-AT could be important to form a stable DeEP.
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An ab initio quantum chemical approach for the modeling of propellant degradation is presented. Using state-of-the-art bonding analysis techniques and composite methods, a series of potential degradation reactions are devised for a sample hydroxyl-terminated-polybutadiene (HTPB) type solid fuel. By applying thermochemical procedures and isodesmic reactions, accurate thermochemical quantities are obtained using a modified G3 composite method based on the resolution of the identity. The calculated heats of formation for the different structures produced presents an â¼2 kcal/mol average error when compared against experimental values.
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Multiple ERI (Electron Repulsion Integral) tensor contractions (METC) with several matrices are ubiquitous in quantum chemistry. In response theories, the contraction operation, rather than ERI computations, can be the major bottleneck, as its computational demands are proportional to the multiplicatively combined contributions of the number of excited states and the kernel pre-factors. This paper presents several high-performance strategies for METC. Optimal approaches involve either the data layout reformations of interim density and Fock matrices, the introduction of intermediate ERI quartet buffer, and loop-reordering optimization for a higher cache hit rate. The combined strategies remarkably improve the performance of the MRSF (mixed reference spin flip)-TDDFT (time-dependent density functional theory) by nearly 300%. The results of this study are not limited to the MRSF-TDDFT method and can be applied to other METC scenarios.
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Although it plays a critical role in the photophysics and catalysis of lanthanides, spin-orbit coupling of electrons on individual lanthanide atoms in small clusters is not well understood. The major objective of this work is to probe such coupling of the praseodymium (Pr) 4f and 6s electrons in Pr2O2 and Pr2O2+. The approach combines mass-analyzed threshold ionization spectroscopy and spin-orbit multiconfiguration second-order quasi-degenerate perturbation theory. The energies of six ionization transitions are precisely measured; the adiabatic ionization energy of the neutral cluster is 38 045 (5) cm-1. Most of the electronic states involved in these transitions are identified as spin-orbit coupled states consisting of two or more electron spins. The electron configurations of these states are 4f46s2 for the neutral cluster and 4f46s for the singly charged cation, both in planar rhombus-type structures. The spin-orbit splitting due to the coupling of the electrons on the separate Pr atoms is on the order of hundreds of wavenumbers.
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Using an OpenMP Application Programming Interface, the resolution-of-the-identity second-order Møller-Plesset perturbation (RI-MP2) method has been off-loaded onto graphical processing units (GPUs), both as a standalone method in the GAMESS electronic structure program and as an electron correlation energy component in the effective fragment molecular orbital (EFMO) framework. First, a new scheme has been proposed to maximize data digestion on GPUs that subsequently linearizes data transfer from central processing units (CPUs) to GPUs. Second, the GAMESS Fortran code has been interfaced with GPU numerical libraries (e.g., NVIDIA cuBLAS and cuSOLVER) for efficient matrix operations (e.g., matrix multiplication, matrix decomposition, and matrix inversion). The standalone GPU RI-MP2 code shows an increasing speedup of up to 7.5× using one NVIDIA V100 GPU with one IBM 42-core P9 CPU for calculations on fullerenes of increasing size from 40 to 260 carbon atoms using the 6-31G(d)/cc-pVDZ-RI basis sets. A single Summit node with six V100s can compute the RI-MP2 correlation energy of a cluster of 175 water molecules using the correlation consistent basis sets cc-pVDZ/cc-pVDZ-RI containing 4375 atomic orbitals and 14 700 auxiliary basis functions in â¼0.85 h. In the EFMO framework, the GPU RI-MP2 component shows near linear scaling for a large number of V100s when computing the energy of an 1800-atom mesoporous silica nanoparticle in a bath of 4000 water molecules. The parallel efficiencies of the GPU RI-MP2 component with 2304 and 4608 V100s are 98.0% and 96.1%, respectively.
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Electronic structure calculations have the potential to predict key matter transformations for applications of strategic technological importance, from drug discovery to material science and catalysis. However, a predictive physicochemical characterization of these processes often requires accurate quantum chemical modeling of complex molecular systems with hundreds to thousands of atoms. Due to the computationally demanding nature of electronic structure calculations and the complexity of modern high-performance computing hardware, quantum chemistry software has historically failed to operate at such large molecular scales with accuracy and speed that are useful in practice. In this paper, novel algorithms and software are presented that enable extreme-scale quantum chemistry capabilities with particular emphasis on exascale calculations. This includes the development and application of the multi-Graphics Processing Unit (GPU) library LibCChem 2.0 as part of the General Atomic and Molecular Electronic Structure System package and of the standalone Extreme-scale Electronic Structure System (EXESS), designed from the ground up for scaling on thousands of GPUs to perform high-performance accurate quantum chemistry calculations at unprecedented speed and molecular scales. Among various results, we report that the EXESS implementation enables Hartree-Fock/cc-pVDZ plus RI-MP2/cc-pVDZ/cc-pVDZ-RIFIT calculations on an ionic liquid system with 623 016 electrons and 146 592 atoms in less than 45 min using 27 600 GPUs on the Summit supercomputer with a 94.6% parallel efficiency.
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A broad range of approaches to many-body dispersion are discussed, including empirical approaches with multiple fitted parameters, augmented density functional-based approaches, symmetry adapted perturbation theory, and a supermolecule approach based on coupled cluster theory. Differing definitions of "body" are considered, specifically atom-based vs molecule-based approaches.
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The aldol reaction of p-nitrobenzaldehyde in amino-catalyzed mesoporous silica nanoparticles (MSN) has revealed varying catalytic activity with the size of the pores of MSN. The pore size dependence related to the reactivity indicates that the diffusion process is important. A detailed molecular-level analysis for understanding diffusion requires assessment of the noncovalent interactions of the molecular species involved in the aldol reaction with each other, with the solvent, and with key functional groups on the pore surface. Such an analysis is presented here based upon the effective fragment potential (EFP). The EFP method can calculate the intermolecular interactions, decomposed into Coulomb, polarization, dispersion, exchange-repulsion, and charge-transfer interactions. In this study, the potential energy surfaces corresponding to each intermolecular interaction are analyzed for homo- and hetero-dimers with various configurations. The monomers that compose dimers are five molecules such as p-nitrobenzaldehyde, acetone, n-hexane, propylamine, and silanol. The results illustrate that the dispersion interaction is crucial in most dimers.
Assuntos
Nanopartículas , Dióxido de Silício , Aldeídos , Porosidade , PropilaminasRESUMO
A generalized, projection-based transformation of the method-agnostic Fock operator in various ab initio fragment-based quantum chemistry methods has been developed for the treatment of interfragment covalent bonds. This transformation freezes the relevant localized molecular orbital associated with each interfragment bond, thereby restricting the variational subspace of the fragment wave functions, in order to maintain the proper physical characteristics of the involved covalent bonds. In addition, sets of orbitals that would lead to multiple occupancy of certain orbitals are explicitly removed from the variational space. The transformation is developed for the specific case of mutually orthonormal frozen and unfrozen orbitals within each fragment. The newly developed approach is then used to study model systems with two popular ab initio fragment-based methods, and the results of these calculations are compared to those obtained by existing methodologies. Analysis is focused on both quantitative and qualitative accuracy as well as computational scalability and stability. Other methods for which the developed formalisms are appropriate are outlined, and future extensions of the methods are discussed.
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The quasi-atomic orbital (QUAO) bonding analysis is used to study intramolecular hydrogen bonding (IMHB) in salicylic acid and an intermediate that is crucial to the synthesis of aspirin. The bonding analysis rigorously explores IMHB through directly accessing information that is intrinsic to the molecular wave function, thereby bypassing the need for intrinsically biased methods. The variables that affect the strength of IMHB are determined using kinetic bond orders, QUAO populations, and QUAO hybridizations. Important properties include both the interatomic distance between hydrogen and oxygen participating in the IMHB and the hybridization on the oxygen. The bonding analysis further shows that each intramolecular hydrogen bond is a four-electron three-center bond. The bonding analysis is used to understand how aromatic reactivity changes due to the effect of functional groups on the aromatic ring.
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Molecular Dynamics (MD) simulations based on the Effective Fragment Potential (EFP) method are utilized to provide a comprehensive assessment of diffusion in liquid n-hexane. We decompose translational diffusion into components along and orthogonal to the long axis of the molecule. Rotational diffusion is decomposed into tumbling and spinning motions about this axis. Our analysis yields four corresponding diffusion coefficients which are related to diagonal entries in the complete 6 × 6 diffusion tensor accounting for the three rotational and three translational degrees of freedom and for the potential coupling between them. However, coupling between different degrees of freedom is expected to be minimal for a natural choice of the molecular body-fixed axis, so then off-diagonal entries in the tensor are negligible. This expectation is supported by a hydrodynamic analysis of the diffusion tensor which treats the liquid surrounding the molecule being tracked as a viscous continuum. Thus, the EFP MD analysis provides a comprehensive characterization of diffusion and also reveals expected shortcomings of the hydrodynamic treatment, particularly for rotational diffusion, when applied to neat liquids.
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The precise ionization energy of praseodymium oxide (PrO) seeded in supersonic molecular beams is measured with mass-analyzed threshold ionization (MATI) spectroscopy. A total of 33 spin-orbit (SO) states of PrO and 23 SO states of PrO+ are predicted by second-order multiconfigurational quasi-degenerate perturbation (MCQDPT2) theory. Electronic transitions from four low-energy SO levels of the neutral molecule to the ground state of the singly charged cation are identified by combining the MATI spectroscopic measurements with the MCQDPT2 calculations. The precise ionization energy is used to reassess the ionization energies and the reaction enthalpies of the Pr + O â PrO+ + e- chemi-ionization reaction reported in the literature. An empirical formula that uses atomic electronic parameters is proposed to predict the ionization energies of lanthanide monoxides, and the empirical calculations match well with available precise experimental measurements.
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Vibronic spectra of lutetium oxide (LuO) seeded in supersonic molecule beams are investigated with mass-analyzed threshold ionization (MATI) spectroscopy and second-order multiconfigurational quasi-degenerate perturbation (MCQDPT2) theory. Six states of LuO and four states of LuO+ are located by the MCQDPT2 calculations, and an a3Π(LuO+) â C2Σ+ (LuΟ) transition is observed by the MATI measurement. The vibronic spectra show abnormal vibrational intervals for both the neural and cation excited states, and the abnormality is attributed to vibrational perturbations induced by interactions with neighboring states.
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The quasi-atomic orbital (QUAO) bonding analysis introduced by Ruedenberg and co-workers is used to develop an understanding of the hydrogen bonds in small water clusters, from the dimer through the hexamer (bag, boat, book, cyclic, prism and cage conformers). Using kinetic bond orders as a metric, it is demonstrated that as the number of waters in simple cyclic clusters increases, the hydrogen bonds strengthen, from the dimer through the cyclic hexamer. However, for the more complex hexamer isomers, the strength of the hydrogen bonds varies, depending on whether the cluster contains double acceptors and/or double donors. The QUAO analysis also reveals the three-center bonding nature of hydrogen bonds in water clusters.