We develop a rigorous quantum mechanical theory for collisions of polyatomic molecular radicals with S-state atoms in the presence of an external magnetic field. The theory is based on a fully uncoupled space-fixed basis set representation of the multichannel scattering wavefunction. Explicit expressions are presented for the matrix elements of the scattering Hamiltonian for spin-1/2 and spin-1 polyatomic molecular radicals interacting with structureless targets. The theory is applied to calculate the cross sections and thermal rate constants for spin relaxation in low-temperature collisions of the prototypical organic molecule methylene [CH2(X)] with He atoms. To this end, two highly accurate three-dimensional potential energy surfaces (PESs) of the He-CH2(X) complex are developed using the state-of-the-art CCSD(T) method and large basis sets. Both PESs exhibit shallow minima and are weakly anisotropic. Our calculations show that spin relaxation in collisions of CH2, CHD, and CD2 molecules with He atoms occurs at a much slower rate than elastic scattering over a large range of temperatures (1 uK -- 1 K) and magnetic fields (0.01 - 1 T), suggesting excellent prospects for cryogenic helium buffer-gas cooling of ground-state ortho-CH2(X) molecules in a magnetic trap. Furthermore, we find that ortho-CH2 undergoes collision-induced spin relaxation much more slowly than para-CH2, which indicates that magnetic trapping can be used to separate nuclear spin isomers of open-shell polyatomic molecules.
Chemistry in the ultracold regime enables fully quantum-controlled interactions between atoms and molecules, leading to the discovery of the hidden mechanisms in chemical reactions which are usually curtained by thermal averaging in the high temperature. Recently a couple of diatomic molecules have been cooled to ultracold regime based on laser cooling techniques, but the chemistry associated with these simple molecules is highly limited. In comparison, free radicals play a major role in many important chemical reactions, but yet to be cooled to submillikelvin temperature. Here we propose a no…
Irradiation of a molecular system by an intense laser field can trigger dynamics of both electronic and nuclear subsystems. The lighter electrons usually move on much faster, attosecond time scale but the slow nuclear rearrangement damps ultrafast electronic oscillations, leading to the decoherence of the electronic dynamics within a few femtoseconds. We show that a simple, single-trajectory semiclassical scheme can evaluate the electronic coherence time in polyatomic molecules accurately by demonstrating an excellent agreement with full-dimensional quantum calculations. In contrast to numeric…
We explore the performance of a statistical learning technique based on Gaussian Process (GP) regression as an efficient non-parametric method for constructing multi-dimensional potential energy surfaces (PES) for polyatomic molecules. Using an example of the molecule N$_4$, we show that a realistic GP model of the six-dimensional PES can be constructed with only 240 potential energy points. We construct a series of the GP models and illustrate the convergence of the accuracy of the resulting surfaces as a function of the number of ${\it ab \ initio}$ points. We show that the GP model based on…
We measure molecular vibrations with femtometer precision using time-resolved x-ray absorption spectroscopy. For a demonstration, a Raman process excites the A$_{1g}$ mode in gas-phase SF$_6$ molecules with an amplitude of $\approx50$ fm, which is probed by a time-delayed soft x-ray pulse at the sulfur $L_{2,3}$-edge. Mapping the extremely small measured energy shifts to internuclear distances requires an understanding of the electronic contributions provided by a many-body ab initio simulation. Our study establishes core-level spectroscopy as a precision tool for time-dependent molecular-stru…
To evaluate vibronic spectra beyond the Condon approximation, we extend the on-the-fly ab initio thawed Gaussian approximation by considering the Herzberg-Teller contribution due to the dependence of the electronic transition dipole moment on nuclear coordinates. The extended thawed Gaussian approximation is tested on electronic absorption spectra of phenyl radical and benzene: Calculated spectra reproduce experimental data and are much more accurate than standard global harmonic approaches, confirming the significance of anharmonicity. Moreover, the extended method provides a tool to quantify…
We have demonstrated that a supersonic beam of methyl radicals (CH$_3$) in the ground rotational state of both $para$ and $ortho$ species has been slowed down to standstill with a magnetic molecular decelerator, and successfully captured spatially in an anti-Helmholtz magnetic trap for $>$ 1 s. The trapped CH$_3$ radicals have a mean translational temperature of about 200 mK with an estimated density of $>5.0\times10^7$ cm$^{-3}$. The methyl radical is an ideal system for the study of cold molecules not only because of its high reactivities at low temperatures, but also because further cooling…
Stereo-Electronic Factors Influencing the Stability of Hydroperoxyalkyl Radicals: Transferability of Chemical Trends across Hydrocarbons and ab initio Methods
Optical control of polyatomic molecules promises new opportunities in precision metrology, fundamental chemistry, quantum information, and many-body science. Contemporary experimental and theoretical efforts have mostly focused on cycling photons via excitation of a single electron localized to an alkaline earth (group 2)-like metal center. In this manuscript, we consider pathways towards optical cycling in polyatomic molecules with multi-electron degrees of freedom, which arise from two or more cycling electrons localized to $p$-block post-transition metal and metalloid (group 13, 14, and 15)…
Spectroscopic and structural properties of methoxymethyl radical (CH$_3$OCH$_2$, RDME) are determined using explicitly correlated ab initio methods. This radical of astrophysical and atmospheric relevance has not been fully characterized at low temperatures, which has delayed the astrophysical searches. We provide rovibrational parameters, excitations to the low energy electronic states, torsional and inversion barriers and low vibrational energy levels. In the electronic ground state (X$^2$A), which appears "clean" from non-adiabatic effects, the minimum energy structure is an asymmetric geom…
We consider collisional studies of linear polyatomic ions immersed in ultracold atomic gases and investigate the intermolecular interactions and chemical reactions of several molecular anions ($\mathrm{OH}^-$, $\mathrm{CN}^-$, $\mathrm{NCO}^-$, $\mathrm{C}_2\mathrm{H}^-$, $\mathrm{C}_4\mathrm{H}^-$) with alkali-metal (Li, Na, K, Rb, Cs) and alkaline-earth-metal (Mg, Ca, Sr, Ba) atoms. State-of-the-art ab initio techniques are applied to compute the potential energy surfaces (PESs) for these systems. The coupled cluster method restricted to single, double, and noniterative triple excitations, C…
We present the first variational calculation of a hot temperature ab initio line list for the CH$_3$ radical. It is based on a high level ab initio potential energy surface and dipole moment surface of CH$_3$ in the ground electronic state. The ro-vibrational energy levels and Einstein $A$ coefficients were calculated using the general-molecule variational approach implemented in the computer program TROVE. Vibrational energies and vibrational intensities are found to be in very good agreement with the available experimental data. The line list comprises 9,127,123 ro-vibrational states ($J\le …
We present a computational investigation of the intramolecular exchange coupling in [LnPc$_2$]$^0$ (Ln = Tb, Dy, Ho, and Er) between the Ln$^{3+}$ 4f electrons and the spin-1/2 radical on the phthalocyanine ligands. A series of ab initio multi-configurational/multi-reference Complete/Restricted Active Space Self-Consistent-Field calculations (CASSCF/RASSCF), including non-perturbative spin--orbit coupling, were performed on [LnPc$_2$]$^0$ and on the smaller model compound [LnPz$_2$]$^0$. We find that the exchange coupling mechanisms are restricted by symmetry, but also dependent on the spin po…
A finite-element Delta-Sternheimer approach for computing accurate all-electron RPA correlation energies of polyatomic molecules
Institute of Physics, Chinese Academy of Sciences（中国科学院物理研究所）；School of Physical Sciences, University of Chinese Academy of Sciences（中国科学院大学物理科学学院）；SKLMS, ICMSEC, NCMIS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences（中国科学院数学与系统科学研究院）；School of Mathematical Sciences, University of Chinese Academy of Sciences（中国科学院大学数学科学学院）
The benzene radical anion is a molecular ion pertinent to several organic reactions, including the Birch reduction of benzene in liquid ammonia. The species exhibits a dynamic Jahn-Teller effect due to its open-shell nature and undergoes pseudorotation of its geometry. Here we characterize the complex electronic structure of this condensed-phase system based on ab initio molecular dynamics simulations and GW calculations of the benzene radical anion solvated in liquid ammonia. Using detailed analysis of molecular and electronic structure, we find that the spatial character of the excess electr…
Extension of the MIRS computer package for the modeling of molecular spectra : from effective to full ab initio ro-vibrational hamiltonians in irreducible tensor form
The excited states of polyatomic systems are rather complex, and often exhibit meta-stable dynamical behaviors. Static analysis of reaction pathway often fails to sufficiently characterize excited state motions due to their highly non-equilibrium nature. Here, we proposed a time series guided clustering algorithm to generate most relevant meta-stable patterns directly from ab initio dynamic trajectories. Based on the knowledge of these meta-stable patterns, we suggested an interpolation scheme with only a concrete and finite set of known patterns to accurately predict the ground and excited st…
Smite: A quasiclassical trajectory (QCT) program for bimolecular collisions and unimolecular dynamics on ab-initio, and machine-learned potential energy surfaces
Belgian Institute for Space Aeronomy (BIRA-IASB)（比利时空间气旋研究所）；Department of Chemistry, KU Leuven（荷语鲁汶大学化学系）
Systematic calculation of molecular vibrational spectra through a complete Morse expansion
我们提出了一种精确和有效的方法来计算分子的振动光谱，基于精确对角化的代数计算矩阵的基础上的权力的莫尔斯坐标。本文主要研究了双原子分子的一维势：作为典型的例子，我们将这种方法应用于标准Lennard-Jones振子和H2分子的从头算势。通过30 x 30矩阵的对角化获得的H2光谱展示了整体cm-1精度。这个理论是在一个新的方法，以获得全球准确的振动光谱数据的背景下的多维潜在的多原子分子，在一个负担得起的计算成本的根源。
Whereas collisions between atoms and molecules are largely understood, collisions between two molecules have proven much harder to study. In both experiment and theory, our ability to determine quantum state-resolved bimolecular cross sections lags behind their atom-molecule counterparts by decades. For many bimolecular systems, even rules of thumb -- much less intuitive understanding -- of scattering cross sections are lacking. Here, we report the measurement of state-to-state differential cross sections on the collision of state-selected and velocity-controlled nitric oxide (NO) radicals and…
Alkaline earth monoalkoxide free radicals (MORs) have molecular properties conducive to direct laser cooling to sub-millikelvin temperatures. Using dispersed laser induced fluorescence (DLIF) measurements from a pulsed supersonic molecular beam source we determine vibrational branching ratios and Franck-Condon factors for the MORs CaOH and CaOCH$_{3}$. With narrow linewidth continuous-wave dye laser excitation, we precisely measure fluorescence branching for both $\tilde{X}-\tilde{A}$ and $\tilde{X}-\tilde{B}$ electronic systems in each molecule. Weak symmetry-forbidden decays to excited bendi…
Finite-Temperature Thermally-Assisted-Occupation Density Functional Theory, Ab Initio Molecular Dynamics, and Quantum Mechanics/Molecular Mechanics Methods
National Taiwan University（台湾大学）；Department of Physics, National Taiwan University（台湾大学物理系）；Center for Theoretical Physics and Center for Quantum Science and Engineering, National Taiwan University（台湾大学理论物理中心与量子科学与工程中心）；Physics Division, National Center for Theoretical Sciences（国家理论科学中心物理组）
Visualizing molecular transformations in real-time requires a structural retrieval method with Ångström spatial and femtosecond temporal atomic resolution. Imaging of hydrogen-containing molecules additionally requires an imaging method that is sensitive to the atomic positions of hydrogen nuclei, with most methods possessing relatively low sensitivity to hydrogen scattering. Laser-induced electron diffraction (LIED) is a table top technique that can image ultrafast structural changes of gas-phase polyatomic molecules with sub-Ångström and femtosecond spatiotemporal resolution together with re…
We consider collisional properties of polyatomic aromatic hydrocarbon molecules immersed into ultracold atomic gases and investigate intermolecular interactions of exemplary benzene, naphthalene, and azulene with alkali-metal (Li, Na, K, Rb, Cs) and alkaline-earth-metal (Mg, Ca, Sr, Ba) atoms. We apply the state-of-the-art \textit{ab initio} techniques to compute the potential energy surfaces (PESs). We use the coupled cluster method restricted to single, double, and noniterative triple excitations to reproduce the correlation energy and the small-core energy-consistent pseudopotentials to mod…
The generalization accuracy of machine learning models of potential energy surfaces (PES) and force fields (FF) for large polyatomic molecules can be generally improved either by increasing the number of training points or by improving the models. In order to build accurate models based on expensive high-level ab initio calculations, much of recent work has focused on the latter. In particular, it has been shown that gradient domain machine learning (GDML) models produce accurate results for high-dimensional molecular systems with a small number of ab initio calculations. The present work exte…
FERM3D: A finite element R-matrix electron molecule scattering code
FERM 3D是一个三维有限元程序，用于计算低能电子与一般多原子分子的弹性散射，并将其转化为势散射问题。该代码是基于球坐标系中的三次多项式。电子-分子相互作用被视为三项之和：静电、交换。和极化。静电项可以直接从从头算代码（{ \sc{GAUSSIAN 98} }在这里描述的工作），而交换项近似使用局部密度泛函。基于密度泛函理论[C.李，W。Yang和R. G. Parr，{Phys. Rev. B} {37}，（1988）785]描述了由散射电子引起的对分子靶的长程吸引。该方法的一般性和简单性是重要的，在扩展电子散射计算更复杂的目标比它是可能的与其他方法。
Reaching high densities is a key step towards cold-collision experiments with polyatomic molecules. We use a cryofuge to load up to 2$\times10^7$ CH$_3$F molecules into a box-like electric trap, achieving densities up to 10$^7$/cm$^3$ at temperatures around 350 mK where the elastic dipolar cross-section exceeds 7$\times$10$^{-12}$cm$^2$. We measure inelastic rate constants below 4$\times$10$^{-8}$cm$^3$/s and control these by tuning a homogeneous electric field that covers a large fraction of the trap volume. Comparison to ab-initio calculations gives excellent agreement with dipolar relaxatio…
We use accurate ab initio and quantum scattering calculations to explore the prospects for sympathetic cooling of the heavy molecular radical SrOH($^2Σ$) by ultracold Li atoms in a magnetic trap. A two-dimensional potential energy surface (PES) for the triplet electronic state of Li-SrOH is calculated ab initio using the partially spin-restricted coupled cluster method with single, double and perturbative triple excitations and a large correlation-consistent basis set. The highly anisotropic PES has a deep global minimum in the skewed Li-HOSr geometry with $D_e=4932$ cm$^{-1}$ and saddle point…
Molecular clouds are the cold regions of the Milky Way where stars form. They are enriched by rather complex molecules. Many of these molecules are believed to be synthesized on the icy surfaces of the interstellar submicron-sized dust grains that permeate the Galaxy. At 10 K thermal desorption is ineffcient and, therefore, why these molecules are found in the cold gas has tantalized astronomers for years. The assumption of the current models, called chemical desorption, is that the molecule formation energy released by the chemical reaction at the grain surface is partially absorbed by the gr…
Hydrogen-atom roaming reactions in water clusters: Unveiling an unusual dimension of water reactivity through first-principles calculations and machine learning
Key Laboratory of Material Simulation Methods & Software of Ministry of Education, College of Physics, Jilin University（教育部材料模拟方法与软件重点实验室，吉林大学物理学院）；Institute of Theoretical Chemistry, College of Chemistry, Jilin University（吉林大学化学学院理论化学研究所）
We present a first-principles molecular dynamics (MD) simulation and expound upon a mechanism of oxygen depletion hypothesis to explain the mitigation of normal tissue injury observed in ultra-high-dose-rate (UHDR) FLASH radiotherapy. We simulated damage to a segment of DNA (also representing other bio-molecules such as RNA and proteins) in a simulation box filled with H$_2$O and O$_2$ molecules. Attoseconds physical interactions (ionizations, electronic and vibrational excitations) were simulated by using the Monte Carlo track structure code Geant4-DNA. Immediately after ionization, {\it ab i…
