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Molecular chirality has traditionally been viewed as a binary property where a molecule is classified as either chiral or achiral, yet in recent decades, mathematical methods for quantifying chirality have been explored. Here, we use toy molecular systems to systematically compare the performance of two state-of-the-art chirality measures: (1) the Continuous Chirality Measure (CCM) and (2) the Chirality Characteristic (χ). We find that both methods exhibit qualitatively similar behavior when applied to simple molecular systems such as a four-site molecule or the polymer double-helix, but we show that the CCM may be more suitable for evaluating the chirality of arbitrary molecules or abstract structures such as normal vibrational modes. We discuss a range of considerations for applying these methods to molecular systems in general, and we provide links to user-friendly codes for both methods. We aim for this paper to serve as a concise resource for scientists attempting to familiarize themselves with these chirality measures or attempting to implement chirality measures in their own work. [ABSTRACT FROM AUTHOR]

Stimulated Raman Adiabatic Passage (STIRAP) and its variants, such as M-type chainwise-STIRAP, allow for efficiently transferring the populations in a multilevel system and have widely been used to prepare molecules in their rovibrational ground state. However, their transfer efficiencies are generally imperfect. The main obstacle is the presence of losses and the requirement to make the dynamics adiabatic. To this end, in the present paper, a new theoretical method is proposed for the efficient and robust creation and detection of deeply bound molecules in three-level Λ-type and five-level M-type systems via "Invariant-based shortcut-to-adiabaticity." In the regime of large detunings, we first reduce the dynamics of three- and five-level molecular systems to those of effective two- and three-level counterparts. By doing so, the major molecular losses from the excited states can be well suppressed. Consequently, the effective two-level counterpart can be directly compatible with two different "Invariant-based Inverse Engineering" protocols; the results show that both protocols give a comparable performance and have a good experimental feasibility. For the effective three-level counterpart, by considering a relation among the four incident pulses, we show that this model can be further generalized to an effective Λ-type one with the simplest resonant coupling. This generalized model permits us to borrow the "Invariant-based Inverse Engineering" protocol from a standard three-level Λ-type system to a five-level M-type system. Numerical calculations show that the weakly bound molecules can be efficiently transferred to their deeply bound states without strong laser pulses, and the stability against parameter variations is well preserved. Finally, the detection of ultracold deeply bound molecules is discussed. [ABSTRACT FROM AUTHOR]

In liquid water, there is a natural tendency to form aggregates that consist of water molecules linked by hydrogen bonds. Such spontaneously formed aggregates are surrounded by a "sea" of disordered water molecules, with both forms remaining in equilibrium. The process of creating water aggregates also takes place in the solvation water of proteins, but in this case, the interactions of water molecules with the protein surface shift the equilibrium of the process. In this paper, we analyze the structural properties of the solvation water in antifreeze proteins (AFPs). The results of molecular dynamics analysis with the use of various parameters related to the structure of solvation water on the protein surface are presented. We found that in the vicinity of the active region responsible for the binding of AFPs to ice, the equilibrium is clearly shifted toward the formation of "ice-like aggregates," and the solvation water has a more ordered ice-like structure. We have demonstrated that a reduction in the tendency to create "ice-like aggregates" results in a significant reduction in the antifreeze activity of the protein. We conclude that shifting the equilibrium in favor of the formation of "ice-like aggregates" in the solvation water in the active region is a prerequisite for the biological functionality of AFPs, at least for AFPs having a well-defined ice binding area. In addition, our results fully confirm the validity of the "anchored clathrate water" concept, formulated by Garnham et al. [Proc. Natl. Acad. Sci. U. S. A. 108, 7363 (2011)]. [ABSTRACT FROM AUTHOR]

This paper presents a comprehensive study of the theory of entangled two-photon emission/absorption (E2P-EA) between a many-level cascade donor and a many-level acceptor (which could be quantum dots or molecules) using second-order perturbation theory and where the donor–acceptor pair is in a homogeneous but dispersive medium. To understand the mechanism of E2P-EA, we analyze how dipole orientation, radiative lifetime, energy detuning between intermediate states, separation distance, and entanglement time impact the E2P-EA rate. Our study shows that there are quantum interference effects in the E2P-EA rate expression that lead to oscillations in the rate as a function of entanglement time. Furthermore, we find that the E2P-EA rate for a representative system consisting of two quantum dots can be comparable to one-photon emission/absorption (OP-EA) when donor and acceptor are within a few nm. However, the E2P-EA rate falls off much more quickly with separation distance than does OP-EA. [ABSTRACT FROM AUTHOR]

Ytterbium monohydroxide is a promising molecule in the search for new physics. It is well known that levels of opposite parity, separated by energy split, the so-called l-doublets, define the experimental electric field strength required for molecule polarization. In addition, in our previous paper [Phys. Rev. A 105, L050801 (2022)], we have shown that the value of l-doubling directly influences the sensitivity of linear triatomic molecules toward the P , T -odd effects. In our work [J. Chem. Phys. 155, 164301 (2021)], we have calculated the value of l-doubling for YbOH molecules with the approximation of fixed O–H bond length. Taking the importance of this property into account, in the present study, we consider the additional degree of freedom corresponding to ligand (OH) deformation. [ABSTRACT FROM AUTHOR]

The article discusses the debate surrounding the mechanism of sum frequency generation (SFG) signals emitted by liquid benzene. The authors argue that the main signal comes from local modes generated by symmetry breaking, while another paper challenges this view and suggests that the dominant mechanism is the interfacial electric quadrupole. The authors refute this argument, stating that their previous paper considered both symmetry breaking and the electric quadrupole in their calculations, while the opposing paper did not properly examine the effect of symmetry breaking. The authors present evidence of symmetry breaking through computational evaluations and the reversal of symmetry breaking at the silica-benzene interface. They recommend that the opposing authors consider these evidences before drawing their conclusion. [Extracted from the article]

This paper demonstrates the performance of our previously suggested property-energy consistent method on the example of the generation of effective basis sets, pecS-1 and pecS-2, suited for the calculation of hydrogen, carbon, nitrogen, and oxygen chemical shifts. The new basis sets were successfully approbated in the GIAO-DFT calculations of the chemical shifts of 35 molecules using six different functionals. The pecS-1 basis set demonstrated very good accuracy, which makes this small basis set an effective means for the large-scale computations. At the same time, the pecS-2 basis set also gave very accurate results, thus putting it on a par with the other commensurate basis sets suited for the chemical shifts calculations. [ABSTRACT FROM AUTHOR]

The theory of adiabatic electron transport in a correlated condensed-matter system is rooted in a seminal paper by Niu and Thouless [J. Phys. A: Math. Gen. 17, 2453 (1984)]; I adopt here an analogous logic in order to retrieve the known expression for the adiabatic electronic flux in a molecular system [L. A. Nafie, J. Chem. Phys. 79, 4950 (1983)]. Its derivation here is considerably simpler than those available in the current quantum-chemistry literature; it also explicitly identifies the adiabaticity parameter, in terms of which the adiabatic flux and the electron density are both exact to first order. It is shown that the continuity equation is conserved to the same order. For the sake of completeness, I also briefly outline the relevance of the macroscopic electronic flux to the physics of solids and liquids. [ABSTRACT FROM AUTHOR]

The Dirac–Coulomb equation with positive-energy projection is solved using explicitly correlated Gaussian functions. The algorithm and computational procedure aims for a parts-per-billion convergence of the energy to provide a starting point for further comparison and further developments in relation with high-resolution atomic and molecular spectroscopy. Besides a detailed discussion of the implementation of the fundamental spinor structure, permutation, and point-group symmetries, various options for the positive-energy projection procedure are presented. The no-pair Dirac–Coulomb energy converged to a parts-per-billion precision is compared with perturbative results for atomic and molecular systems with small nuclear charge numbers. Paper II [D. Ferenc, P. Jeszenszki, and E. Mátyus, J. Chem. Phys. 156, 084110 (2022).] describes the implementation of the Breit interaction in this framework. [ABSTRACT FROM AUTHOR]

We discuss the possibility of using circularly polarized luminescence (CPL) as a tool to probe individual triplet spin sublevels that are populated nonadiabatically following photoexcitation. This study is motivated by a mechanism proposed for chirality-induced spin selectivity in which coupled electronic-nuclear dynamics may lead to a non-statistical population of the three triplet sublevels in chiral systems. We find that low-temperature CPL should aid in quantifying the exact spin state/s populated through coupled electronic-nuclear motion in chiral molecules. [ABSTRACT FROM AUTHOR]

We present a theory for pitch, a matrix property that is linked to the coupling of rotational and translational motion of rigid bodies at low Reynolds numbers. The pitch matrix is a geometric property of objects in contact with a surrounding fluid, and it can be decomposed into three principal axes of pitch and their associated moments of pitch. The moments of pitch predict the translational motion in a direction parallel to each pitch axis when the object is rotated around that axis and can be used to explain translational drift, particularly for rotating helices. We also provide a symmetrized boundary element model for blocks of the resistance tensor, allowing calculation of the pitch matrix for arbitrary rigid bodies. We analyze a range of chiral objects, including chiral molecules and helices. Chiral objects with a Cn symmetry axis with n > 2 show additional symmetries in their pitch matrices. We also show that some achiral objects have non-vanishing pitch matrices, and we use this result to explain recent observations of achiral microswimmers. We also discuss the small but non-zero pitch of Lord Kelvin's isotropic helicoid. [ABSTRACT FROM AUTHOR]

The formation of angulon, stemming from the rotor (molecule or impurity), rotating in the quantum many-body field, adds a new member to the quasi-particles' family and has aroused intense interest in multiple research fields. However, the analysis of the coupling strength between the rotor and its hosting environment remains a challenging task, both in theory and experiment. Here, we develop the all-coupling theory of the angulon by introducing a unitary transformation, where the renormalization of the rotational constants for different molecules in the helium nanodroplets is reproduced, getting excellent agreement with the experimental data collected during the past decades. Moreover, the strength of molecule-helium coupling and the effective radius of the solvation shell co-rotating along with the molecular rotor could be estimated qualitatively. This model not only provides significant enlightenment for analyzing the rotational spectroscopy of molecules in the phononic environment, but also provides a new method to study the transfer of the phonon angular momentum in the angulon frame. [ABSTRACT FROM AUTHOR]

The focal-point approximation can be used to estimate a high-accuracy, slow quantum chemistry computation by combining several lower-accuracy, faster computations. We examine the performance of focal-point methods by combining second-order Møller–Plesset perturbation theory (MP2) with coupled-cluster singles, doubles, and perturbative triples [CCSD(T)] for the calculation of harmonic frequencies and that of fundamental frequencies using second-order vibrational perturbation theory (VPT2). In contrast to standard CCSD(T), the focal-point CCSD(T) method approaches the complete basis set (CBS) limit with only triple-ζ basis sets for the coupled-cluster portion of the computation. The predicted harmonic and fundamental frequencies were compared with the experimental values for a set of 20 molecules containing up to six atoms. The focal-point method combining CCSD(T)/aug-cc-pV(T + d)Z with CBS-extrapolated MP2 has mean absolute errors vs experiment of only 7.3 cm−1 for the fundamental frequencies, which are essentially the same as the mean absolute error for CCSD(T) extrapolated to the CBS limit using the aug-cc-pV(Q + d)Z and aug-cc-pV(5 + d)Z basis sets. However, for H2O, the focal-point procedure requires only 3% of the computation time as the extrapolated CCSD(T) result, and the cost savings will grow for larger molecules. [ABSTRACT FROM AUTHOR]

Heavy-atom alkaline earth monofluoride molecules are considered as prospective systems to study spatial parity or spatial parity and time-reversal symmetry violating effects such as the nuclear anapole moment or the electron electric dipole moment. A comprehensive and highly accurate theoretical study of the electronic structure properties and transition energies in such systems can simplify the preparation and interpretation of the experiments. However, almost no attempts to calculate quantum electrodynamics (QED) effects' contribution into characteristics of these neutral heavy-atom molecules have been performed. Recently, we have formulated and implemented such an approach to calculate QED contributions to transition energies of molecules [L. V. Skripnikov, J. Chem. Phys. 154, 201101 (2021)]. In this paper, we perform a benchmark theoretical study of the transition energies in the Ba+ cation and BaF molecule. The deviation of the calculated values from the experimental ones is of the order 10 cm−1 and is more than an order of magnitude better than the "chemical accuracy," 350 cm−1. The achievement of such an agreement has been provided, in particular, by the inclusion of the QED effects. The latter appeared to be not less important than the high-order correlation effects beyond the coupled cluster with single, double, and perturbative triple cluster amplitude level. We compare the role of QED effects for transition energies with heavier molecules—RaF and E120F, where E120 is the superheavy Z = 120 homolog of Ra. [ABSTRACT FROM AUTHOR]

Chiral molecules have the potential for creating new magnetic devices by locally manipulating the magnetic properties of metallic surfaces. When chiral polypeptides chemisorb onto ferromagnets, they can induce magnetization locally by spin exchange interactions. However, direct imaging of surface magnetization changes induced by chiral molecules was not previously realized. Here, we use magneto-optical Kerr microscopy to image domains in thin films and show that chiral polypeptides strongly pin domains, increasing the coercive field locally. In our study, we also observe a rotation of the easy magnetic axis toward the out-of-plane, depending on the sample's domain size and the adsorption area. These findings show the potential of chiral molecules to control and manipulate magnetization and open new avenues for future research on the relationship between chirality and magnetization. [ABSTRACT FROM AUTHOR]

The prediction of solubilities of compounds by means of molecular simulation has been receiving increasing attention due to the key role played by solubility in countless applications. We have predicted the aqueous solubility of urea at 300 K from chemical potential calculations for two urea model combinations: Özpinar/TIP3P and Hölzl/(TIP4P/2005). The methodology assumes that the intramolecular contribution of the urea molecule to the chemical potentials is identical in the crystal and in solution and, hence, cancels out. In parallel to the chemical potential calculations, we also performed direct coexistence simulations of a urea crystal slab in contact with urea-water solutions with the aim to identify upper and lower bounds to the solubility value using an independent route. The chemical potential approach yielded similar solubilities for both urea models, despite the actual chemical potential values showing a significant dependence on the force field. The predicted solubilities for the two models were 0.013–0.018 (Özpınar) and 0.008–0.012 (Hölzl) mole fraction, which are an order of magnitude lower than the experimental solubility that lies in a range of 0.125–0.216 mole fraction. The direct coexistence solubility bounds were relatively wide and did not encompass the chemical potential based solubilities, although the latter were close to the lower bound values. [ABSTRACT FROM AUTHOR]

Chirality-induced spin selectivity has been attracting extensive interest in recent years and is demonstrated in a variety of chiral molecules, all of which arise from inherent molecular chirality. Here, we first propose a theoretical model to study the spin-dependent electron transport along guanine-quadruplex (G4) DNA molecules, connected to two nonmagnetic electrodes, by considering the molecule–electrode contact and weak spin–orbit coupling. Our results indicate that the G4-DNA molecular junctions exhibit pronounced spin-selectivity effect, and the asymmetric contact-induced external chirality, instead of the inherent molecular chirality, dominates their spin filtration efficiency. Furthermore, the spin-selectivity effect is robust against the disorder and hold in a wide range of model parameters. These results could be checked by charge transport measurements and provide an alternative way to improve the spin-selectivity effect of chiral nanodevices. [ABSTRACT FROM AUTHOR]

We demonstrate the accuracy of ground-state energies of the transcorrelated Hamiltonian, employing sophisticated Jastrow factors obtained from variational Monte Carlo, together with the coupled cluster and distinguishable cluster methods at the level of singles and doubles excitations. Our results show that already with the cc-pVTZ basis, the transcorrelated distinguishable cluster method gets close to the complete basis limit and near full configuration interaction quality values for relative energies of over thirty atoms and molecules. To gauge the performance in different correlation regimes, we also investigate the breaking of the nitrogen molecule with transcorrelated coupled cluster methods. Numerical evidence is presented to further justify an efficient way to incorporate the major effects coming from the three-body integrals without explicitly introducing them into the amplitude equations. [ABSTRACT FROM AUTHOR]

In this contribution, we employ a density matrix-based optimization procedure to obtain customized basis functions to describe chains of rotating water molecules in interaction regimes associated with different intermolecular distances. This procedure is shown to yield a very compact basis with a clear truncation criterion based on the population of the single particle basis functions. For the water trimer, we discuss the convergence behavior of several properties and show it to be superior when compared to an energy-based truncated basis. It is demonstrated that the optimized basis reduces the necessary number of basis functions by at least an order of magnitude. Finally, the optimization procedure is employed to study larger chains of up to ten water molecules. The formation of hydrogen bonds as well as its impact on the net polarization of the chain is discussed. [ABSTRACT FROM AUTHOR]

Quantum annealers are an alternative approach to quantum computing, which make use of the adiabatic theorem to efficiently find the ground state of a physically realizable Hamiltonian. Such devices are currently commercially available and have been successfully applied to several combinatorial and discrete optimization problems. However, the application of quantum annealers to problems in chemistry remains a relatively sparse area of research due to the difficulty in mapping molecular systems to the Ising model Hamiltonian. In this paper, we review two different methods for finding the ground state of molecular Hamiltonians using Ising model-based quantum annealers. In addition, we compare the relative effectiveness of each method by calculating the binding energies, bond lengths, and bond angles of the H 3 + and H2O molecules and mapping their potential energy curves. We also assess the resource requirements of each method by determining the number of qubits and computation time required to simulate each molecule using various parameter values. While each of these methods is capable of accurately predicting the ground state properties of small molecules, we find that they are still outperformed by modern classical algorithms and that the scaling of the resource requirements remains a challenge. [ABSTRACT FROM AUTHOR]

We used Langevin dynamics simulations without hydrodynamic interactions to probe knot diffusion mechanisms and the time scales governing the evolution and the spontaneous untying of trefoil knots in nanochannel-confined DNA molecules in the extended de Gennes regime. The knot untying follows an "opening up process," wherein the initially tight knot continues growing and fluctuating in size as it moves toward the end of the DNA molecule before its annihilation at the chain end. The mean knot size increases significantly and sub-linearly with increasing chain contour length. The knot diffusion in nanochannel-confined DNA molecules is subdiffusive, with the unknotting time scaling with chain contour length with an exponent of 2.64 ± 0.23 to within a 95% confidence interval. The scaling exponent for the mean unknotting time vs chain contour length, along with visual inspection of the knot conformations, suggests that the knot diffusion mechanism is a combination of self-reptation and knot region breathing for the simulated parameters. [ABSTRACT FROM AUTHOR]

An analytic gradient approach for the computation of derivatives of parity-violating (PV) potentials with respect to displacements of the nuclei in chiral molecules is described and implemented within a quasirelativistic mean-field framework. Calculated PV potential gradients are utilized for estimating PV frequency splittings between enantiomers in rotational and vibrational spectra of four chiral polyhalomethanes, i.e., CHBrClF, CHClFI, CHBrFI, and CHAtFI. Values calculated within the single-mode approximation for frequency shifts agree well with previously reported theoretical values. The influence of non-separable anharmonic effects (multi-mode effects) on vibrational frequency shifts, which are readily accessible with the present analytic derivative approach, is estimated for the C–F stretching fundamental of all four molecules and computed for each of the fundamentals in CHBrClF and CHAtFI. Multi-mode effects are found to be significant, in particular, for C–F stretching modes, being for some modes and cases of similar size as the single-mode contribution. [ABSTRACT FROM AUTHOR]

We have evaluated total and partial photoionization cross sections, β asymmetry parameters, and molecular frame photoelectron angular distributions (MFPADs) of the water molecule by using the XCHEM methodology. This method accounts for electron correlation in the electronic continuum, which is crucial to describe Feshbach resonances and their autoionization decay. We have identified a large number of Feshbach resonances, some of them previously unknown, in the region between 12.2 and 18.7 eV, for which we provide energy positions and widths. Many of these resonances lead to pronounced peaks in the photoionization spectra, some of them remarkably wide (up to 0.2 eV, for resonances converging to the third ionization threshold), which should be observable in high-energy resolution experiments. We show that, in the vicinity of these peaks, both asymmetry parameters and MFPADs vary very rapidly with photoelectron energy, which, as in atoms and simpler molecules, reflects the interference between direct ionization and autoionization, which is mostly driven by electron correlation. [ABSTRACT FROM AUTHOR]

This work presents an extension of the projector operator embedding scheme of Manby et al. [J. Chem. Theory Comput. 8, 2564 (2012)] in a multicomponent (MC) framework. Here, a molecular system containing electrons and other types of quantum species is divided into a wavefunction (WF) subsystem of interest and a density functional theory (DFT) environment. The WF-in-DFT partition decreases computational costs by partially truncating the WF subsystem basis set at the cost of introducing a controllable embedding error. To explore the applicability of the MC extension, third-order propagator-in-DFT calculations were performed for positron–anion complexes for alkoxides and carboxylates with carbon chains of different sizes. For these systems, it was found that selecting a WF subsystem with the positron and only the oxygen atoms caused an error of 0.1 eV or lower in positron-binding energies, while reducing between 33% and 55% the basis set size. The reduction of computational costs achieved with the embedding scheme allowed us to improve molecular positron-binding energy predictions by performing complete basis set limit extrapolations. Combining the WF-in-DFT embedding and the complete basis set extrapolation, positronium aliphatic alkoxides were predicted to be energetically stable by 0.3 eV with respect to Ps emission. Similarly, positronium carboxylates, both aromatic and aliphatic, were predicted to be stable by 1.3 eV. [ABSTRACT FROM AUTHOR]

Due to the electron correlation, the fast removal of an electron from a molecule may create a coherent superposition of cationic states and in this way initiate pure electronic dynamics in which the hole-charge left by the ionization migrates throughout the system on an ultrashort time scale. The coupling to the nuclear motion introduces a decoherence that eventually traps the charge, and crucial questions in the field of attochemistry include how long the electronic coherence lasts and which nuclear degrees of freedom are mostly responsible for the decoherence. Here, we report full-dimensional quantum calculations of the concerted electron-nuclear dynamics following outer-valence ionization of propynamide, which reveal that the pure electronic coherences last only 2–3 fs before being destroyed by the nuclear motion. Our analysis shows that the normal modes that are mostly responsible for the fast electronic decoherence are the symmetric in-plane modes. All other modes have little or no effect on the charge migration. This information can be useful to guide the development of reduced dimensionality models for larger systems or the search for molecules with long coherence times. [ABSTRACT FROM AUTHOR]

Recently, Ma et al. [Phys. Rev. Lett. 118, 027402 (2017)] have suggested that water molecules encapsulated in (6,5) single-wall carbon nanotube experience a temperature-induced quasiphase transition around 150 K interpreted as changes in the water dipoles orientation. We discuss further this temperature-driven quasiphase transition performing quantum chemical calculations and molecular dynamics simulations and, most importantly, suggesting a simple lattice model to reproduce the properties of the one-dimensional confined finite arrays of water molecules. The lattice model takes into account not only the short-range and long-range interactions but also the rotations in a narrow tube, and both ingredients provide an explanation for a temperature-driven orientational ordering of the water molecules, which persists within a relatively wide temperature range. [ABSTRACT FROM AUTHOR]

Theoretical analysis and computer simulations (Monte Carlo and numerical integration of differential equations) indicate that the statistical effect of a small number of reacting molecules is affected by transfer of reagent molecules between nanoreactors (droplets in this study). As a model reaction, a simple reversible association A + B ⇆ C was chosen, which was studied previously without reagent transfer processes. For sufficiently fast exchange of reactant molecules and a sufficiently high number of nanoreactors, the studied systems virtually do not differ from large volume systems if overall kinetics and thermodynamics of the chemical process are concerned. However, if either reagent molecule exchange is not fast or the number of exchanging nanoreactors is low, then the stochastic effect is clearly visible, influencing the kinetics of reaching reaction equilibrium. In systems with a low number of nanoreactors, the apparent (average) equilibrium constant is affected as well. The distribution of reactant molecules in the nanoreactors is governed by stochastic processes, dependent on stochastic rate constants of all processes, chemical as well as physical (transfer of molecules outside and into droplets). When accumulation of reactant molecules in the continuous phase cannot be neglected, then the partition coefficients of reactants between the continuous and dispersed phases have to be taken into account. Distributions of reactant molecules described in the paper for systems composed of few nanoreactors can be especially important for some biochemical processes in living cells or devised corresponding artificial reactors. If the reactant molecules predominate in a continuous phase, then the kinetics and overall conversion of reversible association may be significantly affected by the presence of the dispersed phase and its catalytic behavior can be observed. It has been shown that Monte Carlo simulations, applying a devised simple algorithm, give reliable results, allowing theoretical studies of nanoscale-droplet systems. [ABSTRACT FROM AUTHOR]

In this paper, we report a series of transformations for the construction of a Hamiltonian model for nonrigid polyatomic molecules in the framework of the Hougen–Bunker–Johns formalism (HBJ). This model is expressed in normal mode coordinates for small vibrations and in a specific coordinate ρ to describe the large amplitude motion. For the first time, a general procedure linking the "true" curvilinear coordinates to ρ is proposed, allowing the expression of the potential energy part in the same coordinate representation as the kinetic energy operator, whatever the number of atoms. A Lie group-based method is also proposed for the derivation of the reference configuration in the internal axis system. This work opens new perspectives for future high-resolution spectroscopy studies of nonrigid, medium-sized molecules using HBJ-type Hamiltonians. Illustrative examples and computation of vibrational energy levels on semirigid and nonrigid molecules are given to validate this method. [ABSTRACT FROM AUTHOR]

We investigate different approaches to derive the proper Floquet-based quantum–classical Liouville equation (F-QCLE) for laser-driven electron-nuclear dynamics. The first approach projects the operator form of the standard QCLE onto the diabatic Floquet basis and then transforms to the adiabatic representation. The second approach directly projects the QCLE onto the Floquet adiabatic basis. Both approaches yield a form that is similar to the usual QCLE with two modifications: (1) The electronic degrees of freedom are expanded to infinite dimension and (2) the nuclear motion follows Floquet quasi-energy surfaces. However, the second approach includes an additional cross derivative force due to the dual dependence on time and nuclear motion of the Floquet adiabatic states. Our analysis and numerical tests indicate that this cross derivative force is a fictitious artifact, suggesting that one cannot safely exchange the order of Floquet state projection with adiabatic transformation. Our results are in accord with similar findings by Izmaylov et al., [J. Chem. Phys. 140, 084104 (2014)] who found that transforming to the adiabatic representation must always be the last operation applied, although now we have extended this result to a time-dependent Hamiltonian. This paper and the proper derivation of the F-QCLE should lay the basis for further improvements of Floquet surface hopping. [ABSTRACT FROM AUTHOR]

In this paper, we examine decay and fragmentation of core-excited and core-ionized water molecules combining quantum chemical calculations and electron-energy-resolved electron–ion coincidence spectroscopy. The experimental technique allows us to connect electronic decay from core-excited states, electronic transitions between ionic states, and dissociation of the molecular ion. To this end, we calculate the minimum energy dissociation path of the core-excited molecule and the potential energy surfaces of the molecular ion. Our measurements highlight the role of ultra-fast nuclear motion in the 1 a 1 − 1 4 a 1 core-excited molecule in the production of fragment ions. OH+ fragments dominate for spectator Auger decay. Complete atomization after sequential fragmentation is also evident through detection of slow H+ fragments. Additional measurements of the non-resonant Auger decay of the core-ionized molecule (1 a 1 − 1 ) to the lower-energy dication states show that the formation of the OH+ + H+ ion pair dominates, whereas sequential fragmentation OH+ + H+ → O + H+ + H+ is observed for transitions to higher dication states, supporting previous theoretical investigations. [ABSTRACT FROM AUTHOR]

As of yet, unexamined aluminum bearing molecules may help elucidate aluminum chemistry and associated refractory atom reactions in the interstellar medium. The flexibility of modern quantum chemistry in the construction and analysis of novel molecules makes it perfectly suited to analyze molecules of astrochemical significance. In this paper, high level ab initio electronic structure calculations using the coupled cluster CCSD(T) and explicitly correlated coupled cluster CCSD(T)-F12 methods with large basis sets extrapolated to the complete basis set limit have been performed on the various [Al,N,C,O] isomers. The anharmonic rotational and vibrational spectroscopic parameters for all isomers are produced with these same levels of theory via quartic force fields and vibrational perturbation theory in order to aid in their potential laboratory or even astrophysical identification. The most stable isomer is determined here to be the aluminum isocyanate radical with linear equilibrium geometry AlNCO (X1Σ+). The NCO antisymmetric stretch of AlNCO has an intensity of 1500 km/mol, which should greatly aid in its infrared detection in the region around 2305 cm−1. Additionally, the AlOCN isomer is relatively low lying, possesses a 5.12 D dipole moment, and has a notable kinetic stability, making it a viable candidate for astronomical observation. All isomers are characterized by small frequencies, which indicates that these are floppy molecules. Isomers with a terminal aluminum atom are especially floppy, with bending modes less than 100 cm−1. [ABSTRACT FROM AUTHOR]

The centrosymmetric benzene molecule has zero first-order electric dipole hyperpolarizability, which results in no sum-frequency vibrational spectroscopy (SFVS) signal at interfaces, but it shows very strong SFVS experimentally. We perform a theoretical study on its SFVS, which is in good agreement with the experimental results. Its strong SFVS mainly comes from the interfacial electric quadrupole hyperpolarizability rather than the symmetry-breaking electric dipole, bulk electric quadrupole, and interfacial and bulk magnetic dipole hyperpolarizabilities, which provides a novel and completely unconventional point of view. [ABSTRACT FROM AUTHOR]

Intra- and inter-molecular electronic energy current is formulated by defining the probability current of electronic energy, called the energy flux. Among vast possible applications to electronic energy transfer phenomena, including chemical reaction dynamics, here we present a first numerical example from highly excited nonadiabatic electron wavepacket dynamics of a boron cluster B12. [ABSTRACT FROM AUTHOR]

The GW approximation is considered to be the simplest approximation within Hedin's formulation of many-body perturbation theory. It is expected that some of the deficiencies of the GW approximation can be overcome by adding the so-called vertex corrections. In this work, the recently implemented G 0 W 0 Γ 0 (1) scheme, which incorporates the vertex effects by adding the full second-order self-energy correction to the GW self-energy, is applied to a set of first-row transition-metal monoxide (TMO) anions. Benchmark calculations show that results obtained by G 0 W 0 Γ 0 (1) on top of the B3LYP hybrid functional starting point (SP) are in good agreement with experiment data, giving a mean absolute error of 0.13 eV for a testset comprising the ionization energies (IEs) of 27 outer valence molecular orbitals (MOs) from nine TMO anions. A systematic SP-dependence investigation by varying the ratio of the exact exchange (EXX) component in the PBE0-type SP reveals that, for G 0 W 0 Γ 0 (1) , the best accuracy is achieved with 20% EXX. Further error analysis in terms of the orbital symmetry characteristics (i.e., σ, π, or δ) in the testset indicates the best amount of EXX in the SP for G 0 W 0 Γ 0 (1) calculations is independent of MO types, and this is in contrast with the situation in G0W0 calculations, where the best EXX ratio varies for different classes of MOs. Despite its success in describing the absolute IE values, we, however, found that G 0 W 0 Γ 0 (1) faces difficulties in describing the energy separations between certain states of interest, worsening the already underestimated G0W0 predictions. [ABSTRACT FROM AUTHOR]

The molecular electronic wave functions are expressed in quasi-atomic form. The corresponding global energy expression exhibits the unified resolution of the various modes of chemical bonding in terms of physical interactions. The bonding patterns in several molecules is elucidated. [ABSTRACT FROM AUTHOR]

We introduce an extension to the PySCF package, which makes it automatically differentiable. The implementation strategy is discussed, and example applications are presented to demonstrate the automatic differentiation framework for quantum chemistry methodology development. These include orbital optimization, properties, excited-state energies, and derivative couplings, at the mean-field level and beyond, in both molecules and solids. We also discuss some current limitations and directions for future work. [ABSTRACT FROM AUTHOR]

Two-dimensional infrared (2DIR) spectroscopy has become an established method for generating vibrational spectra in condensed phase samples composed of mixtures that yield heavily congested infrared and Raman spectra. These condensed phase 2DIR spectrometers can provide very high temporal resolution (<1 ps), but the spectral resolution is generally insufficient for resolving rotational peaks in gas phase spectra. Conventional (1D) rovibrational spectra of gas phase molecules are often plagued by severe spectral congestion, even when the sample is not a mixture. Spectral congestion can obscure the patterns in rovibrational spectra that are needed to assign peaks in the spectra. A method for generating high resolution 2DIR spectra of gas phase molecules has now been developed and tested using methane as the sample. The 2D rovibrational patterns that are recorded resemble an asterisk with a center position that provides the frequencies of both of the two coupled vibrational levels. The ability to generate easily recognizable 2D rovibrational patterns, regardless of temperature, should make the technique useful for a wide range of applications that are otherwise difficult or impossible when using conventional 1D rovibrational spectroscopy. [ABSTRACT FROM AUTHOR]

While the behavior of active colloidal molecules is well studied now for constant activity, the effect of activity gradients is much less understood. Here, we explore one of the simplest molecules in activity gradients, namely active chiral dimers composed of two particles with opposite active torques of the same magnitude. We show analytically that with increasing torque, the dimer switches its behavior from antichemotactic to chemotactic. The origin of the emergent chemotaxis is the cooperative exploration of an activity gradient by the two particles. While one of the particles moves into higher activity regions, the other moves towards lower activity regions, resulting in a net bias in the direction of higher activity. We do a comparative study of chiral active particles with charged Brownian particles under a magnetic field and show that despite the fundamental similarity in terms of their odd-diffusive behavior, their dynamics and chemotactic behavior are generally not equivalent. We demonstrate this explicitly in a dimer composed of oppositely charged active particles, which remains antichemotactic to any magnetic field. [ABSTRACT FROM AUTHOR]

The structural, electronic, and optical properties of CdSe/CdS core–shell colloidal quantum dot molecules, a new class of coupled quantum dot dimers, are explored using atomistic approaches. Unlike the case of dimers grown by molecular beam epitaxy, simulated strain profile maps of free-standing colloidal dimers show negligible additional strain resulting from the attachment. The electronic properties of the relaxed dimers are described within a semiempirical pseudopotential model combined with the Bethe–Salpeter equation within the static screening approximation to account for electron–hole correlations. The interplay of strain, hybridization (tunneling splitting), quantum confinement, and electron–hole binding energies on the optical properties is analyzed and discussed. The effects of the dimensions of the neck connecting the two quantum dot building blocks, as well as the shell thickness, are studied. [ABSTRACT FROM AUTHOR]

The molecular-scale growth kinetics of ice from water in the presence of air molecules are still poorly understood, despite their importance for understanding ice particle formation in nature. In this study, a molecular dynamics simulation is conducted to elucidate the molecular-scale growth kinetics at the interface between a (111) plane of cubic ice and water in the presence of N2 molecules. Two potential models of N2 molecules with and without atomic charges are examined. For both models, N2 molecules bind stably to the interface for a period of 1 ns or longer, and the stability of the binding is higher for the charged model than for the noncharged model. Free-energy surfaces of an N2 molecule along the interface and along an ideal (111) plane surface of cubic ice suggest that for both models, the position where an N2 molecule binds stably is different at the interface and on the ideal plane surface, and the stability of the binding is much higher for the interface than for the ideal plane surface. For both models, stacking-disordered ice grows at the interface, and the formation probability of a hexagonal ice layer in the stacking-disordered ice is higher for the charged model than for the uncharged model. The formation probability for the hexagonal ice layer in the stacking-disordered ice depends not only on the stability of binding but also on the positions where N2 molecules bind to the underlying ice and the number of N2 molecules that bind stably to the underlying ice. [ABSTRACT FROM AUTHOR]

In a recent communication [N. Makri, J. Chem. Phys. 148, 101101 (2018)], it was shown that the locality of interactions in many systems of interest allows a decomposition of the path integral and its evaluation via sequential linking of the paths of relatively small "modules" (e.g., chemical groups or monomers). The present paper describes the modular path integral methodology for simulating dynamical properties by propagating the density matrix in real time. The procedure is first presented for the simple topology of a single-file arrangement of units interacting via nearest neighbor couplings and subsequently extended to the calculation of two-particle correlations in arrays that may also contain some long-range interactions, to the treatment of systems with side chains or cyclic structures, to the simulation of internal dynamics in long organic molecules, and to the modifications required for coupling of one or several units of a system to dissipative environments. Illustrative applications to the dynamics of interacting two-level-systems are presented. [ABSTRACT FROM AUTHOR]

The ab initio GW plus Bethe–Salpeter equation (GW-BSE, where G is the one particle Green's function and W is the screened Coulomb interaction) approach has emerged as a leading method for predicting excitations in both solids and molecules with a predictive power contingent upon several factors. Among these factors are the (1) generalized Kohn–Sham eigensystem used to construct the GW self-energy and to solve the BSE and (2) the efficacy and suitability of the Tamm–Dancoff approximation. Here, we present a detailed benchmark study of low-lying singlet excitations from a generalized Kohn–Sham (gKS) starting point based on an optimally tuned range-separated hybrid (OTRSH) functional. We show that the use of this gKS starting point with one-shot G0W0 and G0W0-BSE leads to the lowest mean absolute errors (MAEs) and mean signed errors (MSEs), with respect to high-accuracy reference values, demonstrated in the literature thus far for the ionization potentials of the GW100 benchmark set and for low-lying neutral excitations of Thiel's set molecules in the gas phase, without the need for self-consistency. The MSEs and MAEs of one-shot G0W0-BSE@OTRSH excitation energies are comparable to or lower than those obtained with other functional starting points after self-consistency. Additionally, we compare these results with linear-response time-dependent density functional theory (TDDFT) calculations and find GW-BSE to be superior to TDDFT when calculations are based on the same exchange-correlation functional. This work demonstrates tuned range-separated hybrids used in combination with GW and GW-BSE can greatly suppress starting point dependence for molecules, leading to accuracy similar to that for higher-order wavefunction-based theories for molecules without the need for costlier iterations to self-consistency. [ABSTRACT FROM AUTHOR]

In this work, a general tight-binding based energy decomposition analysis (EDA) scheme for intermolecular interactions is proposed. Different from the earlier version [Xu et al., J. Chem. Phys. 154, 194106 (2021)], the current tight-binding based density functional theory (DFTB)-EDA is capable of performing interaction analysis with all the self-consistent charge (SCC) type DFTB methods, including SCC-DFTB2/3 and GFN1/2-xTB, despite their different formulas and parameterization schemes. In DFTB-EDA, the total interaction energy is divided into frozen, polarization, and dispersion terms. The performance of DFTB-EDA with SCC-DFTB2/3 and GFN1/2-xTB for various interaction systems is discussed and assessed. [ABSTRACT FROM AUTHOR]

There has been great progress in developing methods for machine-learned potential energy surfaces. There have also been important assessments of these methods by comparing so-called learning curves on datasets of electronic energies and forces, notably the MD17 database. The dataset for each molecule in this database generally consists of tens of thousands of energies and forces obtained from DFT direct dynamics at 500 K. We contrast the datasets from this database for three "small" molecules, ethanol, malonaldehyde, and glycine, with datasets we have generated with specific targets for the potential energy surfaces (PESs) in mind: a rigorous calculation of the zero-point energy and wavefunction, the tunneling splitting in malonaldehyde, and, in the case of glycine, a description of all eight low-lying conformers. We found that the MD17 datasets are too limited for these targets. We also examine recent datasets for several PESs that describe small-molecule but complex chemical reactions. Finally, we introduce a new database, "QM-22," which contains datasets of molecules ranging from 4 to 15 atoms that extend to high energies and a large span of configurations. [ABSTRACT FROM AUTHOR]

Dispersion interactions are one of the components of van der Waals (vdW) forces that play a key role in the understanding of intermolecular interactions in many physical, chemical, and biological processes. The theory of dispersion forces was developed by London in the early years of quantum mechanics. However, it was only in the 1960s that it was recognized that for molecules lacking an inversion center, such as chiral and helical molecules, there are chirality-sensitive corrections to the dispersion forces proportional to the rotatory power known from the theory of circular dichroism and with the same distance scaling law R−6 as the London energy. The discovery of the chirality-induced spin selectivity effect in recent years has led to an additional twist in the study of chiral molecular systems, showing a close relation between spin and molecular geometry. Motivated by it, we propose in this investigation to describe the mutual induction of charge and spin-density fluctuations in a pair A–B of chiral molecules by a simple physical model. The model assumes that the same fluctuating electric fields responsible for vdW forces can induce a magnetic response via a Rashba-like term so that a spin–orbit field acting on molecule B is generated by the electric field arising from charge density fluctuations in molecule A (and vice versa). Within a second-order perturbative approach, these contributions manifest as an effective intermolecular exchange interaction. Although expected to be weaker than the standard London forces, these interactions display the same R−6 distance scaling. [ABSTRACT FROM AUTHOR]

The phase diagram (pressure versus temperature) of the pure fluid is typically envisioned as being featureless apart from the presence of the liquid-vapor coexistence curve terminating at the critical point. However, a number of recent authors have proposed that this simple picture misses important features, such as the Widom line, the Fisher-Widom line, and the Frenkel line. In our paper, we discuss another way of augmenting the pure fluid phase diagram, lines of zero thermodynamic curvature R = 0 separating regimes of fluid solid-like behavior (R > 0) from gas-like or liquid-like behavior (R < 0). We systematically evaluate R for the 121 pure fluids in the NIST/REFPROP (version 9.1) fluid database near the saturated vapor line from the triple point to the critical point. Our specific goal was to identify regions of positive R abutting the saturated vapor line ("feature D"). We found the following: (i) 97/121 of the NIST/REFPROP fluids have feature D. (ii) The presence and character of feature D correlates with molecular complexity, taken to be the number of atoms Q per molecule. (iii) The solid-like properties of feature D might be attributable to a mesoscopic model based on correlations among coordinated spinning molecules, a model that might be testable with computer simulations. (iv) There are a number of correlations between thermodynamic quantities, including the acentric factor →, but we found little explicit correlation between → and the shape of a molecule. (v) Feature D seriously constrains the size of the asymptotic fluid critical point regime, possibly resolving a long-standing mystery about why these are so small. (vi) Feature D correlates roughly with regimes of anomalous sound propagation. [ABSTRACT FROM AUTHOR]

We investigate the secondary (β-) relaxations of an asymmetric binary glass former consisting of a spirobichroman derivative (SBC; Tg = 356 K) as the high-Tg component and the low-Tg component tripropyl phosphate (TPP; Tg = 134 K). The main relaxations are studied in Paper I [B. Potzschner et al., J. Chem. Phys. 146, 164503 (2017)]. A high Tg contrast of ΔTg = 222 K is put into effect in a non-polymeric system. Component-selective studies are carried out by combining results from dielectric spectroscopy (DS) for mass concentrations cTPP ≤ 60% and those from different methods of 2H and 31P NMR spectroscopy. In the case of NMR, the full concentration range (10% ≤ cTPP ≤ 100%) is covered. The neat components exhibit β-relaxation (β 1 (SBC) and β 2 (TPP)). The latter is rediscovered by DS in the mixtures for all concentrations with unchanged time constants. NMR spectroscopy identifies the β-relaxations as being alike to those in neat glasses. A spatially highly restricted motion with angular displacement below ±10° encompassing all molecules is involved. In the lowtemperature range, where TPP shows the typical 31PNMRecho spectra of the α2-process, very similar spectral features are observed for the (deuterated) SBC component by 2H NMR, in addition to its "own" β 1-process observed at high temperatures. Apparently, the small TPP molecules enslave the large SBC molecules to perform a common hindered reorientation. The temperature dependence of the spin-lattice relaxation time of both components is the same and reveals an angular displacement of the SBC molecules somewhat smaller than that of TPP, though the time constants τβ2 are the same. Furthermore, T1 (T) of TPP in the temperature region of the β 2-process is absolutely the same as in the mixture TPP/polystyrene investigated previously. It appears that the manifestations of the β-process introduced by one component are essentially independent of the second component. Finally, at cTPP ≤ 20% one finds indications that the β 2-process starts to disintegrate. More and more TPP molecules get immobilized upon decreasing cTPP. We conclude that the β-process is a cooperative process. [ABSTRACT FROM AUTHOR]

In this paper, we present new ideas for computing rovibrational energy levels of molecules composed of two components and apply them to H2O-Cl-. When both components are themselves molecules, Euler angles that specify their orientation with respect to an axis system attached to the inter-monomer vector are used as vibrational coordinates. For H2O-Cl-, there is only one set of Euler angles. Using Euler angles as intermolecular vibrational coordinates is advantageous because in many cases coupling between them and coordinates that describe the shape of the monomers is unimportant. The monomers are not assumed to be rigid. In the most efficient calculation, vibrational wavefunctions of the monomers are used as contracted basis functions. Energy levels are calculated using the Lanczos algorithm. [ABSTRACT FROM AUTHOR]

Chemistry is governed by the principle of quantum mechanics as expressed by the Schrödinger equation (SE) and Dirac equation (DE). The exact general theory for solving these fundamental equations is therefore a key for formulating accurately predictive theory in chemical science. The free-complement (FC) theory for solving the SE of atoms and molecules proposed by one of the authors is such a general theory. On the other hand, the working theory most widely used in chemistry is the chemical formula that refers to the molecular structural formula and chemical reaction formula, collectively. There, the central concepts are the local atomic concept, transferability, and from-atoms- to-molecule concept. Since the chemical formula is the most successful working theory in chemistry ever existed, we formulate our FC theory to have the structure reflecting the chemical formula. Our basic postulate is that as far as the SE is the principle of chemistry, its solutions for chemistry should have the structure that can be related to the chemical formulas. So, in this paper, we first formulate a theory that designs the wave function to reflect the structure of the chemical formula. We call this theory chemical formula theory (CFT). In the CFT, we place the valence ground and excited states of each atom at each position of the chemical formula of the molecule and let them interact using their free valences to form the ground and excited states of the molecule. The principle there is the variational principle so that the ground and excited states obtained satisfy the orthogonality and Hamiltonian-orthogonality relations. Then, we formulate the exact FC theory starting from the initial functions produced by the CFT. This FC theory is referred to as free-complement chemical- formula theory (FC-CFT), which is expected to describe efficiently the solution of the SE by the above reason. The FC-CFT wave function is modified from that of CFT. Since this modification is done by the exact SE, its analysis may give some insights to chemists that assist their chemistry. Thus, this theory would be not only exact but also conceptually useful. Furthermore, the intermediate theory between CFT and FC-CFT would also be useful. There, we use only integratable functions and apply the variational principle so that we refer to this theory as FC-CFT-variational (FC-CFT-V). It is an advanced theory of CFT. Since the variational method is straightforward and powerful, we can do extensive chemical studies in a reasonable accuracy. After finishing such studies, if we still need an exact level of solutions, we add the remaining functions of the FC-CFT and perform the exact calculations. Furthermore, when we deal with large and even giant molecules, the inter-exchange (iExg) theory for the antisymmetry rule introduced previously leads to a large simplification. There, the inter-exchanges between distant electron pairs fade away so that only Coulombic interactions survive. Further in giant systems, even an electrostatic description becomes possible. Then, the FC-CFT for exactly solving the SE would behave essentially to order N for large and giant molecular systems, though the pre-factor should be very large and must be minimized. [ABSTRACT FROM AUTHOR]

Fluctuating hydrodynamics (FHD) provides a framework for modeling microscopic fluctuations in a manner consistent with statistical mechanics and nonequilibrium thermodynamics. This paper presents an FHD formulation for isothermal reactive incompressible liquid mixtures with stochastic chemistry. Fluctuating multispecies mass diffusion is formulated using a Maxwell–Stefan description without assuming a dilute solution, and momentum dynamics is described by a stochastic Navier–Stokes equation for the fluid velocity. We consider a thermodynamically consistent generalization for the law of mass action for non-dilute mixtures and use it in the chemical master equation (CME) to model reactions as a Poisson process. The FHD approach provides remarkable computational efficiency over traditional reaction-diffusion master equation methods when the number of reactive molecules is large, while also retaining accuracy even when there are as few as ten reactive molecules per hydrodynamic cell. We present a numerical algorithm to solve the coupled FHD and CME equations and validate it on both equilibrium and nonequilibrium problems. We simulate a diffusively driven gravitational instability in the presence of an acid-base neutralization reaction, starting from a perfectly flat interface. We demonstrate that the coupling between velocity and concentration fluctuations dominates the initial growth of the instability. [ABSTRACT FROM AUTHOR]