Methylene: A Paradigm for Computational Quantum Chemistry

In Silico Chemical Experiments in the Age of AI: From Quantum Chemistry to Machine Learning and Back

Computational chemistry is an indispensable tool for understanding molecules and predicting chemical properties. However, traditional computational methods face significant challenges due to the difficulty of solving the Schrödinger equations and the increasing computational cost with the size of the molecular system. In response, there has been a surge of interest in leveraging artificial intelligence (AI) and machine learning (ML) techniques to in silico experiments. Integrating AI and ML into computational chemistry increases the scalability and speed of the exploration of chemical space. However, challenges remain, particularly regarding the reproducibility and transferability of ML models. This review highlights the evolution of ML in learning from, complementing, or replacing traditional computational chemistry for energy and property predictions. Starting from models trained entirely on numerical data, a journey set forth toward the ideal model incorporating or learning the physical laws of quantum mechanics. This paper also reviews existing computational methods and ML models and their intertwining, outlines a roadmap for future research, and identifies areas for improvement and innovation. Ultimately, the goal is to develop AI architectures capable of predicting accurate and transferable solutions to the Schrödinger equation, thereby revolutionizing in silico experiments within chemistry and materials science.

Natural resonance-theoretic conceptions of extreme electronic delocalization in soft materials

In the broad context of Dalton's atomic hypothesis and subsequent classical vs. quantum understanding of macroscopic materials, we show how Pauling's resonance-type conceptions, as quantified in natural resonance theory (NRT) analysis of modern wavefunctions, can be modified to unify description of interatomic interactions from the Lewis-like limit of localized e-pair covalency in molecules to the extreme delocalized limit of supramolecular "soft matter" aggregation. Such "NRT-centric" integration of NRT bond orders for hard- and soft-matter interactions is illustrated with application to a long-predicted and recently synthesized organometallic sandwich-type complex ("diberyllocene") that exhibits bond orders ranging from the soft limit (bBeC ≈ 0.01) to the typical values (bCC ≈ 1.35) of molecular resonance-covalency in the organic domain, with intermediate value (bBeBe ≈ 0.86) for intermetallic Be⋯Be interaction.

Spectroscopy and Photochemistry of OAlNO and Implications for New Metal Chemistry in the Atmosphere

A new aluminum-bearing species, OAlNO, which has the potential to impact the chemistry of the Earth's upper atmosphere, is characterized via high-level, ab initio, spectroscopic methods. Meteor-ablated aluminum atoms are quickly oxidized to aluminum oxide (AlO) in the mesosphere and lower thermosphere (MLT), where a steady-state layer of AlO then builds up. Concurrent formation of nitric oxide (NO) in the same region of the atmosphere will lead to the bimolecular formation of the OAlNO molecule. Molecular orbital analysis provides fundamental insights into the chemical bonding and energetic arrangement of the triplet (1 3A″) ground state and singlet (1 1A') excited-state species of OAlNO. Additionally, unpaired electrons on the terminal oxygen atom of triplet (1 3A″) OAlNO cause it to be reactive to atmospheric species, potentially impacting climate science and high-altitude chemistry. The triplet (1 3A″) ground-state species exhibits a large permanent dipole moment useful for rotational spectroscopic detection; however, similar rotational constants to the singlet (1 1A') excited-state species will hamper differentiation in a spectrum. Strong infrared intensities will assist in detection and discrimination of the different spin states and isomers. Repulsive electronic excited states of OAlNO will lead to photolysis of the Al-N bond and formation of various electronic states of AlO + NO through nonadiabatic pathways. Reaction through the OAlNO intermediate represents a means for the production of electronically excited AlO, leading to new chemistry in the atmosphere. Excitation to higher-lying electronic states will lead to fluorescence with a minor Stokes shift, useful for laboratory investigation. Such physical properties of this molecule will allow for new, unexplored chemical pathways in the MLT to be considered.

Excited States, Symmetry Breaking, and Unphysical Solutions in State-Specific CASSCF Theory

State-specific electronic structure theory provides a route toward balanced excited-state wave functions by exploiting higher-energy stationary points of the electronic energy. Multiconfigurational wave function approximations can describe both closed- and open-shell excited states and avoid the issues associated with state-averaged approaches. We investigate the existence of higher-energy solutions in complete active space self-consistent field (CASSCF) theory and characterize their topological properties. We demonstrate that state-specific approximations can provide accurate higher-energy excited states in H₂ (6-31G) with more compact active spaces than would be required in a state-averaged formalism. We then elucidate the unphysical stationary points, demonstrating that they arise from redundant orbitals when the active space is too large or symmetry breaking when the active space is too small. Furthermore, we investigate the singlet-triplet crossing in CH₂ (6-31G) and the avoided crossing in LiF (6-31G), revealing the severity of root flipping and demonstrating that state-specific solutions can behave quasi-diabatically or adiabatically. These results elucidate the complexity of the CASSCF energy landscape, highlighting the advantages and challenges of practical state-specific calculations.

Applications of the Spectral Theory of Chemical Bonding to Simple Hydrocarbons

The finite-basis, pair formulation of the Spectral Theory of chemical bonding is briefly surveyed. Solutions of the Born-Oppenheimer polyatomic Hamiltonian that are totally antisymmetric in electron exchange are obtained from diagonalization of an aggregate matrix built up from conventional diatomic solutions to atom-localized problems. A succession of transformations of the bases of the underlying matrices and the unique character of symmetric orthogonalization in producing the archived matrices calculated "once-of-all" in the pairwise-antisymmetrized basis are described. Application is made to molecules containing hydrogens and a single carbon atom. Results in conventional orbital bases are given and compared to experimental and high-level theoretical results. Chemical valence is shown to be respected and subtle angular effects in polyatomic contexts are reproduced. Means of reducing the size of the atomic-state basis and improving the fidelity of the diatomic descriptions for fixed basis size, so as to enable application to larger polyatomic molecules, are outlined along with future initiatives and prospects.

Experimental and Computational Mechanistic Study of Carbonazidate-Initiated Cascade Reactions

A variety of Huisgen cyclization or nitrene/carbene alkyne cascade reactions with different types of termination were investigated. Accessible nitrene precursors were assessed, and carbonazidates were found to be the only effective initiators. Solvents, terminal alkynyl substituents, and catalysts can all impact the reaction outcome. Study of the mechanism both computationally (by density functional theory) and experimentally revealed relevant intermediates and plausible reaction pathways.

High-resolution infrared spectroscopy of supersonically cooled singlet carbenes: Bromomethylene (HCBr) in the CH stretch region

First high-resolution spectra of cold (∼35 K) singlet bromomethylene HCBr in the CH stretching (v₁) region from 2770 to 2850 cm^-1 are reported using near quantum shot-noise limited laser absorption methods in a slit jet supersonic discharge expansion source. Three rovibrational bands are identified at high S/N (20:1-40:1) and rotationally assigned to (i) the CH stretch fundamental (v₁) band X̃1,0,0←X̃0,0,0 and (ii) vibrational hot bands [X̃(1,1,0)←X̃(0,1,0) and X̃(1,0,1)←X̃(0,0,1)] arising from vibrationally excited HCBr populated in the discharge with single quanta in either the H-C-Br bend (v₂) or C-Br stretch (v₃) modes. Precision rotational constants are reported for a total of six states, with an experimentally determined CH stretch vibrational frequency (2799.38 cm^-1) in good agreement with previous low-resolution fluorescence studies [M. Deselnicu et al., J. Chem. Phys. 124(13), 134302 (2006)]. Detailed analysis of the fundamental v₁ band highlights the presence of perturbations in the X̃1,0,0 level, which we tentatively attribute to arise from the nearby triplet state ã(0,0,1) through spin-orbit interaction or the multiple quanta X̃0,2,1 singlet state via c-type Coriolis coupling. Reduced-Doppler resolution (60 MHz) in the slit-jet IR spectrometer permits for clear observation of a nuclear spin hyperfine structure, with experimental line shapes well reproduced by nuclear quadrupole/spin-rotation coupling constants from microwave studies [C. Duan et al., J. Mol. Spectrosc. 220(1), 113-121 (2003)]. Finally, the a-type to b-type transition intensity ratio for the fundamental CH stretch band is notably larger than that predicted by using a bond-dipole model, which from high level ab initio quantum calculations [CCSD(T)/PVQZ] can be attributed to vibrationally induced "charge-sloshing" of electron density along the polar C-Br bond.

Biomolecular modeling thrives in the age of technology

The biomolecular modeling field has flourished since its early days in the 1970s due to the rapid adaptation and tailoring of state-of-the-art technology. The resulting dramatic increase in size and timespan of biomolecular simulations has outpaced Moore's law. Here, we discuss the role of knowledge-based versus physics-based methods and hardware versus software advances in propelling the field forward. This rapid adaptation and outreach suggests a bright future for modeling, where theory, experimentation and simulation define three pillars needed to address future scientific and biomedical challenges.

The challenging playground of astrochemistry: an integrated rotational spectroscopy - quantum chemistry strategy

While it is now well demonstrated that the interstellar medium (ISM) is characterized by a diverse and complex chemistry, a significant number of features in radioastronomical spectra are still unassigned and call for new laboratory efforts, which are increasingly based on integrated experimental and computational strategies. In parallel, the identification of an increasing number of molecules containing more than five atoms and at least one carbon atom (the so-called "interstellar" complex organic molecules), which can play a relevant role in the chemistry of life, raises the additional issue of how these species can be produced in the typical harsh conditions of the ISM. On these grounds, this perspective aims to present an integrated rotational spectroscopy - quantum chemistry approach for supporting radioastronomical observations and a computational strategy for contributing to the elucidation of chemical reactivity in the interstellar space.

Relatives of cyanomethylene: replacement of the divalent carbon by B-, N+, Al-, Si, P+, Ga-, Ge, and As. Phys Chem Chem Phys 2019;21:26438-26452. [PMID: 31774089 DOI: 10.1039/c9cp05777c]

The lowest lying singlet and triplet states of HBCN-, HCCN, HNCN+, HAlCN-, HSiCN, HPCN+, HGaCN-, HGeCN, and HAsCN+ were studied using the CCSDT(Q)/CBS//CCSD(T)/aug-cc-pVQZ level of theory. Periodic trends in geometries, singlet-triplet gaps, and barriers to linearity were established and analyzed. The first row increasingly favors the triplet state, with a singlet-triplet gap (ΔEST = Esinglet - Etriplet) of 3.5 kcal mol-1, 11.9 kcal mol-1, and 22.6 kcal mol-1, respectively, for HBCN-, HCCN, and HNCN+. The second row increasing favors the singlet state, with singlet-triplet gaps of -20.4 kcal mol-1 (HAlCN-), -26.6 kcal mol-1 (HSiCN), and -26.8 kcal mol-1 (HPCN+). The third row also favors the singlet state, with singlet-triplet gaps of -26.8 kcal mol-1 (HGaCN-), -33.5 kcal mol-1 (HGeCN), and -33.1 kcal mol-1 (HAsCN+). The HXCN species have larger absolute singlet-triplet energy gaps compared to their parent species XH2 except for the case of X = N+. The effect of the substitution of hydrogen with a cyano group was analyzed with isodesmic bond separation analysis and NBO.

Infrared spectroscopy of jet-cooled HCCl singlet chlorocarbene diradical: CH stretching and vibrational coupling dynamics

Quantum shot noise limited laser absorption methods are used to obtain first high-resolution infrared rovibrational spectra of jet cooled chlorocarbene (HCCl) diradical in a supersonic slit-jet discharge expansion spectrometer. The rotationally resolved absorption spectra of the C-H stretch ν₁ fundamental are analyzed in the framework of a Watson non-rigid asymmetric rotor Hamiltonian model. Further analysis of the mid-infrared data reveals the additional presence of what has nominally been assigned as the X̃(012) combination band with one quantum of the H-C-Cl bend (ν₂) and two quanta of the C-Cl stretch (2ν₃). Rovibrational constants are obtained from least squares fits for each of the four excited vibrational states built on the ν₁ fundamental X̃(100) and the X̃(012) combination mode for each ³⁵Cl and ³⁷Cl atom isotopologue. The four bands occur within a narrow spectral window, requiring detailed comparison of multiple spectral properties (e.g., rotational constant dependence on vibrational excitation, band types/transition dipole moment alignment in the body-fixed frame, etc.) to aid in the vibrational assignment. Indeed, the IR transition intensities arise from strong anharmonic mixing between the "bright" ν₁ C-H stretch and "dark" X̃012 H-C-Cl bend/C-Cl stretch combination modes, resulting in nearly equal amplitudes for the zeroth order X̃(100) and X̃012 harmonic states. Finally, to aid the spectral search for HCCl in the interstellar medium, ground state two-line combination differences are combined with previous laser-induced fluorescence results to predict precision microwave transitions for HC³⁵Cl and HC³⁷Cl.

Anisotropic and amphoteric characteristics of diverse carbenes

The singlet/triplet stabilities and amphoteric behaviors of diverse carbenes are elucidated with the anisotropic natures of their electron configurations.

Computational organic chemistry: bridging theory and experiment in establishing the mechanisms of chemical reactions

Understanding the mechanisms of chemical reactions, especially catalysis, has been an important and active area of computational organic chemistry, and close collaborations between experimentalists and theorists represent a growing trend. This Perspective provides examples of such productive collaborations. The understanding of various reaction mechanisms and the insight gained from these studies are emphasized. The applications of various experimental techniques in elucidation of reaction details as well as the development of various computational techniques to meet the demand of emerging synthetic methods, e.g., C-H activation, organocatalysis, and single electron transfer, are presented along with some conventional developments of mechanistic aspects. Examples of applications are selected to demonstrate the advantages and limitations of these techniques. Some challenges in the mechanistic studies and predictions of reactions are also analyzed.

A perspective on physical organic chemistry

A perspective on the development of mechanistic carbene chemistry is presented. The author will point out questions that have been answered, and a next generation of questions will be proposed.

QM/MM investigations of organic chemistry oriented questions

About 35 years after its first suggestion, QM/MM became the standard theoretical approach to investigate enzymatic structures and processes. The success is due to the ability of QM/MM to provide an accurate atomistic picture of enzymes and related processes. This picture can even be turned into a movie if nuclei-dynamics is taken into account to describe enzymatic processes. In the field of organic chemistry, QM/MM methods are used to a much lesser extent although almost all relevant processes happen in condensed matter or are influenced by complicated interactions between substrate and catalyst. There is less importance for theoretical organic chemistry since the influence of nonpolar solvents is rather weak and the effect of polar solvents can often be accurately described by continuum approaches. Catalytic processes (homogeneous and heterogeneous) can often be reduced to truncated model systems, which are so small that pure quantum-mechanical approaches can be employed. However, since QM/MM becomes more and more efficient due to the success in software and hardware developments, it is more and more used in theoretical organic chemistry to study effects which result from the molecular nature of the environment. It is shown by many examples discussed in this review that the influence can be tremendous, even for nonpolar reactions. The importance of environmental effects in theoretical spectroscopy was already known. Due to its benefits, QM/MM can be expected to experience ongoing growth for the next decade.In the present chapter we give an overview of QM/MM developments and their importance in theoretical organic chemistry, and review applications which give impressions of the possibilities and the importance of the relevant effects. Since there is already a bunch of excellent reviews dealing with QM/MM, we will discuss fundamental ingredients and developments of QM/MM very briefly with a focus on very recent progress. For the applications we follow a similar strategy.

THEORETICAL INVESTIGATION OF METHYLENE: USING ULTRAHIGH ACCURATE MRCI APPROACH

A new hybrid vairational-perturbational MRCISD(TQ) approach is applied to the problem of singlet–triplet and singlet–singlet separation in methylene using several basis sets. The inclusion of higher excitations beyond single and double excitations can predict more accurate splitting energies between states as well as closer single-point energies to available full CI results when the small basis set is used. Comparisons with MRCISD and MRCCSD treatments indicate that MRCISD(TQ) can lead to reliable predictions of the splitting energies when larger bases are employed.

Biomolecularmodeling and simulation: a field coming of age

We assess the progress in biomolecular modeling and simulation, focusing on structure prediction and dynamics, by presenting the field’s history, metrics for its rise in popularity, early expressed expectations, and current significant applications. The increases in computational power combined with improvements in algorithms and force fields have led to considerable success, especially in protein folding, specificity of ligand/biomolecule interactions, and interpretation of complex experimental phenomena (e.g. NMR relaxation, protein-folding kinetics and multiple conformational states) through the generation of structural hypotheses and pathway mechanisms. Although far from a general automated tool, structure prediction is notable for proteins and RNA that preceded the experiment, especially by knowledge-based approaches. Thus, despite early unrealistic expectations and the realization that computer technology alone will not quickly bridge the gap between experimental and theoretical time frames, ongoing improvements to enhance the accuracy and scope of modeling and simulation are propelling the field onto a productive trajectory to become full partner with experiment and a field on its own right.

Spin-state splittings, highest-occupied-molecular-orbital and lowest-unoccupied-molecular-orbital energies, and chemical hardness

It is known that the exact density functional must give ground-state energies that are piecewise linear as a function of electron number. In this work we prove that this is also true for the lowest-energy excited states of different spin or spatial symmetry. This has three important consequences for chemical applications: the ground state of a molecule must correspond to the state with the maximum highest-occupied-molecular-orbital energy, minimum lowest-unoccupied-molecular-orbital energy, and maximum chemical hardness. The beryllium, carbon, and vanadium atoms, as well as the CH(2) and C(3)H(3) molecules are considered as illustrative examples. Our result also directly and rigorously connects the ionization potential and electron affinity to the stability of spin states.