By leveraging the fundamental doctrine of The Quantum Theory of Atoms in Molecules---the partitioning of the electron charge density ($ρ$) into regions bounded by surfaces of zero flux---we map the gradient field of $ρ$ onto a 2D space called the gradient bundle condensed charge density ($\cal{P}$). The topology of $\cal{P}$ appears to correlate with regions of chemical significance in $ρ$. The bond wedge is defined as the image in $ρ$ of the basin of attraction in $\cal{P}$, analogous to the Bader atom, which is the basin of attraction in $ρ$. A bond bundle is defined as the union of bond wedges that share interatomic surfaces. We show that maxima in $\cal{P}$ typically map to bond paths in $ρ$, though this is not necessarily always true. This observation addresses many of the concerns regarding the chemical significance of bond critical points and bond paths in The Quantum Theory of Atoms in Molecules.
We examine the dynamics of chiral states of chiral molecules with high tunneling rates in dilute and condensed phases in the context of time-dependent perturbation theory. The chiral molecule is effectively described by an asymmetric double-well potential, whose asymmetry is a measure of chiral interactions. The dilute and condensed phases are conjointly described by a collection of harmonic oscillators but respectively with temperature-dependent sub-ohmic and temperature-independent ohmic spectral densities. We examine our method quantitatively by applying the dynamics to isotopic ammonia mol…
A quantum system composed of a molecule and an atomic ensemble, confined in a microscopic cavity, is investigated theoretically. The indirect coupling between atoms and the molecule, realized by their interaction with the cavity radiation mode, leads to a coherent mixing of atomic and molecular states, and at strong enough cavity field strengths hybrid atom-molecule-photon polaritons are formed. It is shown for the Na$_2$ molecule that by changing the cavity wavelength and the atomic transition frequency, the potential energy landscape of the polaritonic states and the corresponding spectrum c…
Partial atomic charges belong to key concepts of computational chemistry. In some cases, however, they fail in describing the electrostatics of molecules. One such example is the $σ$-hole, a region of positive electrostatic potential located on halogens and other atoms. In molecular mechanics, the $σ$-hole is often modeled as a pseudo-atom with a positive partial charge located off the halogen nucleus. Here we address a question, to what extent the pseudo-atom affects partial charges of other atoms in the molecule. To this aim, we have thoroughly analyzed partial charges of over 2300 halogenat…
The orientational correlation scheme introduced earlier for tetrahedral molecules is extended for being able to classify orientational correlations between pairs of high symmetry molecules. While in the original algorithm a given orientation of a pair of tetrahedral molecules is characterized unambiguously by the number of ligand atoms that can be found between two planes that contain each centre and perpendicular to the centre-centre connecting line, in the generalized algorithm, the planes are replaced by cones, whose apex angles are set according to the symmetry of each molecule. To demonst…
We introduce machine learning models of quantum mechanical observables of atoms in molecules. Instant out-of-sample predictions for proton and carbon nuclear chemical shifts, atomic core level excitations, and forces on atoms reach accuracies on par with density functional theory reference. Locality is exploited within non-linear regression via local atom-centered coordinate systems. The approach is validated on a diverse set of 9k small organic molecules. Linear scaling of computational cost in system size is demonstrated for saturated polymers with up to sub-mesoscale lengths.
Mid-infrared (mid-IR) spectroscopy provides a way to study structures and dynamics of complicated molecules in condensed phases. Therefore, developing compact and broadband mid-IR spectrometer has been a long-standing challenge. Here, we show that a highly coherent and broadband mid-IR frequency comb can be generated by using an intra-pulse difference-frequency-generation with a train of pulses from a few-cycle Ti:Sapphire oscillator. By tightly focusing the oscillator output beam into a single-pass fan-out-type periodically-poled lithium niobate crystal and tilting the orientation of the crys…
A method of slowing, accelerating, cooling, and bunching molecules and neutral atoms using time-varying electric field gradients is demonstrated with cesium atoms in a fountain. The effects are measured and found to be in agreement with calculation. Time-varying electric field gradient slowing and cooling is applicable to atoms that have large dipole polarizabilities, including atoms that are not amenable to laser slowing and cooling, to Rydberg atoms, and to molecules, especially polar molecules with large electric dipole moments. The possible applications of this method include slowing and c…
When designing molecular functional materials, the properties of the active specie, the dye, must be optimized fully accounting for environmental effects. Here we present an effective model to account for the spectroscopic effects of the medium electronic polarizability on the properties of charge-transfer dyes. Different classes of molecules are considered and the proposed antiadiabatic approach to solvation is contrasted with the adiabatic approach, currently adopted in all quantum chemical approaches to solvation. Transition frequencies and band-shapes are addressed, and the role of the med…
Density functional theory (DFT) calculation has had huge success as a tool capable of predicting important physical and chemical properties of condensed matter systems. We calculate the electric dipole moment of a molecule by using the differential electron density with respect to the superimposed electron density of the free atoms, exploiting the cancellation of DFT errors. Our results on a range of molecules show an excellent agreement with experiments.
We theoretically examine two-color photoassociation of a Bose-Einstein condensate, focusing on the role of rogue decoherence in the formation of macroscopic atom-molecule superpositions. Rogue dissociation occurs when two zero-momentum condensate atoms are photoassociated into a molecule, which then dissociates into a pair of atoms of equal-and-opposite momentum, instead of dissociating back to the zero-momentum condensate. As a source of decoherence that may damp quantum correlations in the condensates, rogue dissociation is an obstacle to the formation of a macroscopic atom-molecule superpos…
The proposed paradigm of plasmonic atoms and plasmonic molecules allows one to describe and predict the strongly localized plasmonic oscillations in the clusters of nanoparticles and some other nanostructures in uniform way. Strongly localized plasmonic molecules near the contacting surfaces might become the fundamental elements (by analogy with Lego bricks) for a construction of fully integrated opto-electronic nanodevices of any complexity and scale of integration.
Alkaline-earth-like transition-metal atoms such as Zn and Cd are promising candidates for precision measurements and quantum many-body physics experiments. Here, we theoretically investigate the properties of diatomic molecules containing these closed-shell atoms. We calculate potential energy curves, permanent electric dipole moments, and spectroscopic constants for molecules consisting of either a Zn or Cd atom interacting with an alkali-metal (Li, Na, K, Rb, Cs, Fr) or alkaline-earth-metal (Be, Mg, Ca, Sr, Ba, Ra) atom. We use the ab initio electronic structure coupled cluster method with s…
A highly sensitive, general, and preferably nondestructive technique to detect polar molecules would greatly advance a number of fields, in particular quantum science with cold and ultracold molecules. Here, we propose using resonant energy transfer between molecules and Rydberg atoms to detect molecules. Based on an energy transfer cross section of $>10^{-6}\,$cm$^2$ for sufficiently low collision energies, a near unit efficiency non-destructive detection of basically any polar molecule species in a well defined internal state should be possible.
We theoretically examine photoassociation of a non-ideal Bose-Einstein condensate, focusing on evidence for a macroscopic superposition of atoms and molecules. This problem raises an interest because, rather than two states of a given object, an atom-molecule system is a seemingly impossible macroscopic superposition of different objects. Nevertheless, photoassociation enables coherent intraparticle conversion, and we thereby propose a viable scheme for creating a superposition of a macroscopic number of atoms with a macroscopic number of molecules.
Recent studies illustrate how machine learning (ML) can be used to bypass a core challenge of molecular modeling: the tradeoff between accuracy and computational cost. Here, we assess multiple ML approaches for predicting the atomization energy of organic molecules. Our resulting models learn the difference between low-fidelity, B3LYP, and high-accuracy, G4MP2, atomization energies, and predict the G4MP2 atomization energy to 0.005 eV (mean absolute error) for molecules with less than 9 heavy atoms and 0.012 eV for a small set of molecules with between 10 and 14 heavy atoms. Our two best model…
We provide a physical interpretation of the Kirchhoff index of any molecules as well as of the Wiener index of acyclic ones. For the purpose, we use a local vertex invariant that is obtained from first principles and describes the atomic displacements due to small vibrations/oscillations of atoms from their equilibrium positions. In addition, we show that the topological atomic displacements correlate with the temperature factors (B-factors) of atoms obtained by X-ray crystallography for both organic molecules and biological macromolecules.
We theoretically investigate Raman photoassociation of a degenerate Bose-Fermi mixture of atoms and the subsequent prospect for anomalous (Cooper) pairing between atoms and molecules. Stable fermionic molecules are created via free-bound-bound stimulated Raman adiabatic passage which, in contrast to purely bosonic systems, can occur in spite of collisions. With the leftover atomic condensate to enhance intrafermion interactions, the superfluid transition to atom-molecule Cooper pairs occurs at a temperature that is roughly an order of magnitude below what is currently feasible.
