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A generative model for molecule generation based on chemical reaction trees

Dai Hai Nguyen, Koji Tsuda

Deep generative models have been shown powerful in generating novel molecules with desired chemical properties via their representations such as strings, trees or graphs. However, these models are limited in recommending synthetic routes for the generated molecules in practice. We propose a generative model to generate molecules via multi-step chemical reaction trees. Specifically, our model first propose a chemical reaction tree with predicted reaction templates and commercially available molecules (starting molecules), and then perform forward synthetic steps to obtain product molecules. Experiments show that our model can generate chemical reactions whose product molecules are with desired chemical properties. Also, the complete synthetic routes for these product molecules are provided.

10.1063/5.0076749

Dissociation and Decay of Ultra-cold Sodium Molecules

T. Mukaiyama, J. R. Abo-Shaeer, K. Xu, J. K. Chin, W. Ketterle

The dissociation of ultracold molecules is studied by ramping an external magnetic field through a Feshbach resonance. The observed dissociation energy shows non-linear dependence on the ramp speed and directly yields the strength of the atom-molecule coupling. In addition, inelastic molecule-molecule and molecule-atom collisions are characterized.

10.1103/PhysRevLett.92.180402

IMG2SMI: Translating Molecular Structure Images to Simplified Molecular-input Line-entry System

Daniel Campos, Heng Ji

Like many scientific fields, new chemistry literature has grown at a staggering pace, with thousands of papers released every month. A large portion of chemistry literature focuses on new molecules and reactions between molecules. Most vital information is conveyed through 2-D images of molecules, representing the underlying molecules or reactions described. In order to ensure reproducible and machine-readable molecule representations, text-based molecule descriptors like SMILES and SELFIES were created. These text-based molecule representations provide molecule generation but are unfortunately rarely present in published literature. In the absence of molecule descriptors, the generation of molecule descriptors from the 2-D images present in the literature is necessary to understand chemistry literature at scale. Successful methods such as Optical Structure Recognition Application (OSRA), and ChemSchematicResolver are able to extract the locations of molecules structures in chemistry papers and infer molecular descriptions and reactions. While effective, existing systems expect chemists to correct outputs, making them unsuitable for unsupervised large-scale data mining. Leveraging the task formulation of image captioning introduced by DECIMER, we introduce IMG2SMI, a model which leverages Deep Residual Networks for image feature extraction and an encoder-decoder Transformer layers for molecule description generation. Unlike previous Neural Network-based systems, IMG2SMI builds around the task of molecule description generation, which enables IMG2SMI to outperform OSRA-based systems by 163% in molecule similarity prediction as measured by the molecular MACCS Fingerprint Tanimoto Similarity. Additionally, to facilitate further research on this task, we release a new molecule prediction dataset. including 81 million molecules for molecule description generation

Orientational orders in binary mixtures of hard HGO molecules

Xin Zhou, Hu Chen, Mitsumasa Iwamoto

studied liquid crystal phases of binary mixtures of non-spherical molecules. The components of the mixtures are two kinds of hard Gaussian overlap (HGO) molecules, one kind of molecules with a small molecular-elongation parameter (small HGO molecules) cannot form stable liquid crystal phase in bulk, and other with a large elongation parameter (large HGO molecules) can form liquid crystal phase easily. In the mixtures, like the large HGO molecules, the small HGO molecules can also form an orientation-ordered phase, which is because that the large HGO molecules can form complex confining surfaces to induce the alignment of the small molecules and generate an isotropic-anisotropic phase transition in the whole binary mixtures. We also study the transition on different mixtures composed of small and large HGO molecules with different elongations and different concentrations of the large molecules. The obtained result implies that small anisotropic molecules might show liquid crystal behavior in confinement.

10.1063/1.1634954

Pulling short DNA molecules having defects on different locations

Amar Singh, Navin Singh

We present a study on the role of defects on the stability of short DNA molecules. We consider short DNA molecules (16 base pairs) and investigate the thermal as well as mechanical denaturation of these molecules in the presence of defects that occurs anywhere in the molecule. For the investigation, we consider four different kinds of chains. Not only the ratio of AT to GC different in these molecules but also the distributions of AT and GC along the molecule are different. With suitable modifications in the statistical model to show the defect in a pair, we investigate the denaturation of short DNA molecules in thermal as well as constant force ensemble. In the force ensemble, we pulled the DNA molecule from each end (keeping other end free) and observed some interesting features of opening of the molecule in the presence of defects in the molecule. We calculate the probability of opening of the DNA molecule in the constant force ensemble to explain the opening of base pairs and hence the denaturation of molecules in the presence of defects.

Phys. Rev. E, v92, p03270, 2015

10.1103/PhysRevE.92.032703

On the molecules of numerical semigroups, Puiseux monoids, and Puiseux algebras

Felix Gotti, Marly Gotti

A molecule is a nonzero non-unit element of an integral domain (resp., commutative cancellative monoid) having a unique factorization into irreducibles (resp., atoms). Here we study the molecules of Puiseux monoids as well as the molecules of their corresponding semigroup algebras, which we call Puiseux algebras. We begin by presenting, in the context of numerical semigroups, some results on the possible cardinalities of the sets of molecules and the sets of reducible molecules (i.e., molecules that are not irreducibles/atoms). Then we study the molecules in the more general context of Puiseux monoids. We construct infinitely many non-isomorphic atomic Puiseux monoids all whose molecules are atoms. In addition, we characterize the molecules of Puiseux monoids generated by rationals with prime denominators. Finally, we turn to investigate the molecules of Puiseux algebras. We provide a characterization of the molecules of the Puiseux algebras corresponding to root-closed Puiseux monoids. Then we use such a characterization to find an infinite class of Puiseux algebras with infinitely many non-associated reducible molecules.

Numerical Semigroups (Editors: V. Barucci, S. T. Chapman, M. D'Anna, and R. Froberg), Springer INdAM Series, Vol. 40, Switzerland, 2020

Electronic structure of ultralong-range Rydberg pentaatomic molecules with two polar diatomic molecules

Javier Aguilera-Fernández, H. R. Sadeghpour, Peter Schmelcher, Rosario González-Férez

We explore the electronic structure of ultralong-range pentaatomic Rydberg molecules from a merger of a Rydberg atom and two ground state heteronuclear diatomic molecules. Our focus is on the interaction of Rb($23s$) and Rb($n=20$, $l\ge 3$) Rydberg states with ground and rotationally excited KRb diatomic polar molecules. For symmetric and asymmetric configurations of the pentaatomic Rydberg molecule, we investigate the metamorphosis of the Born-Oppenheimer potential curves, essential for the binding of the molecule, with varying distance from the Rydberg core and analyze the alignment and orientation of the polar diatomic molecules.

Phys. Rev. A 96, 052509 (2017)

10.1103/PhysRevA.96.052509

Soliton molecules in Sharma-Tasso-Olver-Burgers equation

Zhaowen Yan, Senyue Lou

Soliton molecules have been experimentally discovered in optics and theoretically investigated for coupled systems. This paper is concerned with the formation of soliton molecules by the resonant mechanism for a noncoupled system, the Sharma-Tasso-Olver-Burgers (STOB) equation. In terms of introducing velocity resonance conditions, we derive the soliton (kink) molecules, half periodic kink (HPK) molecules and breathing soliton molecule of STOB equation. Meanwhile, the fission and fusion phenomena among kinks, kink molecules, HPKs and HPK molecules have been revealed. Moreover, we also discuss the central periodic kink solutions from the multiple solitary wave solutions.

Probabilistic Optically-Selective Single-molecule Imaging Based Localization Encoded (POSSIBLE) Microscopy for Ultra-superresolution Imaging

Partha Pratim Mondal

To be able to resolve molecular-clusters it is crucial to access vital informations (such as, molecule density and cluster-size) that are key to understand disease progression and the underlying mechanism. Traditional single-molecule localization microscopy (SMLM) techniques use molecules of variable sizes (as determined by its localization precisions (LPs)) to reconstruct super-resolution map. This results in an image with overlapping and superimposing PSFs (due to a wide size-spectrum of single molecules) that degrade image resolution. Ideally it should be possible to identify the brightest molecules (also termed as, fortunate molecules) to reconstruct ultra-superresolution map, provided sufficient statistics is available from the recorded data. POSSIBLE microscopy explores this possibility by introducing narrow probability size-distribution of single molecules (narrow size-spectrum about a predefined mean-size). The reconstruction begins by presetting the mean and variance of the narrow distribution function (Gaussian function). Subsequently, the dataset is processed and single molecule filtering is carried out by the Gaussian distribution function to filter out unfortunate molecules. The fortunate molecules thus retained are then mapped to reconstruct ultra-superresolution map. In-principle, the POSSIBLE microscopy technique is capable of infinite resolution (resolution of the order of actual single molecule size) provided enough fortunate molecules are experimentally detected. In short, bright molecules (with large emissivity) holds the key. Here, we demonstrate the POSSIBLE microscopy technique and reconstruct single molecule images with an average PSF sizes of 15 nm, 30 nm and 50 nm. Results show better-resolved Dendra2-HA clusters with large cluster-density in transfected NIH3T3 fibroblast cells as compared to the traditional SMLM techniques.

10.1371/journal.pone.0242452

Evidence for association of triatomic molecule in ultracold $^{23}$Na$^{40}$K and $^{40}$K mixture

Huan Yang, Xin-Yao Wang, Zhen Su, Jin Cao, De-Chao Zhang, Jun Rui, Bo Zhao, Chun-Li Bai, Jian-Wei Pan

Ultracold assembly of diatomic molecules has enabled great advances in controlled chemistry, ultracold chemical physics, and quantum simulation with molecules. Extending the ultracold association to triatomic molecules will offer many new research opportunities and challenges in these fields. A possible approach is to form triatomic molecules in the ultracold atom and diatomic molecule mixture by employing the Feshbach resonance between them. Although the ultracold atom-diatomic-molecule Feshbach resonances have been observed recently, utilizing these resonances to form triatomic molecules remains challenging. Here we report on the evidence of the association of triatomic molecules near the Feshbach resonances between $^{23}$Na$^{40}$K molecules in the rovibrational ground state and $^{40}$K atoms. We apply a radio-frequency pulse to drive the free-bound transition and monitor the loss of $^{23}$Na$^{40}$K molecules. The association of triatomic molecules manifests itself as an additional loss feature in the radio-frequency spectra, which can be distinguished from the atomic loss feature.The binding energy of triatomic molecule is estimated from the measurement. Our work is helpful to understand the complex ultracold atom-molecule Feshbach resonance and may open up an avenue towards the preparation and control of ultracold triatomic molecules.

Nature 602, 229 (2022)

10.1038/s41586-021-04297-2

Exciton Binding Energy in small organic conjugated molecule

Pabitra K. Nayak

For small organic conjugated molecules the exciton binding energy can be calculated treating molecules as conductor, and is given by a simple relation BE \approx e2/(4{\pi}{\epsilon}0{\epsilon}R), where {\epsilon} is the dielectric constant and R is the equivalent radius of the molecule. However, if the molecule deviates from spherical shape, a minor correction factor should be added.

Arrangement of DOBAMBC molecules inside the capsule on change of the molecule's inclination on the border of the capsule investigated by the molecular dynamics method

M. A. Korshunov

The method of molecular dynamics is used to investigate the distribution of DOBAMBC molecules in a capsule with the fixed border layer. Change of an arrangement of molecules in smectic layers depending on an inclination of molecules on border is considered.

Microwave traps for cold polar molecules

D. DeMille, D. R. Glenn, J. Petricka

We discuss the possibility of trapping polar molecules in the standing-wave electromagnetic field of a microwave resonant cavity. Such a trap has several novel features that make it very attractive for the development of ultracold molecule sources. Using commonly available technologies, microwave traps can be built with large depth (up to several Kelvin) and acceptance volume (up to several cm^3), suitable for efficient loading with currently available sources of cold polar molecules. Unlike most previous traps for molecules, this technology can be used to confine the strong-field seeking absolute ground state of the molecule, in a free-space maximum of the microwave electric field. Such ground state molecules should be immune to inelastic collisional losses. We calculate elastic collision cross-sections for the trapped molecules, due to the electrical polarization of the molecules at the trap center, and find that they are extraordinarily large. Thus, molecules in a microwave trap should be very amenable to sympathetic and/or evaporative cooling. The combination of these properties seems to open a clear path to producing large samples of polar molecules at temperatures much lower than has been possible previously.

10.1140/epjd/e2004-00163-6

Competition of Chiroptical Effect Caused by Nanostructure and Chiral Molecules

Tong Wu, Jun Ren, Rongyao Wang, Xiangdong Zhang

The theory to calculate circular dichroism (CD) of chiral molecules in a finite cluster with arbitrarily disposed objects has been developed by means of T-matrix method. The interactions between chiral molecules and nanostructures have been investigated. Our studies focus on the case of chiral molecules inserted into plasmonic hot spots of nanostructures. Our results show that the total CD of the system with two chiral molecules is not sum for two cases when two chiral molecules inserted respectively into the hot spots of nanoparticle clusters as the distances among nanoparticles are small, although the relationship is established at the case of large interparticle distances. The plasmonic CD arising from structure chirality of nanocomposites depends strongly on the relative positions and orientations of nanospheroids, and are much greater than that from molecule-induced chirality. However, the molecule-induced plasmonic CD effect from the molecule-NP nanocomposites with special chiral structures can be spectrally distinguishable from the structure chirality-based optical activity. Our results provide a new theoretical framework for understanding the two different aspects of plasmonic CD effect in molecule-NP nanocomposites, which would be helpful for the experimental design of novel biosensors to realize ultrasensitive probe of chiral information of molecules by plasmon-based nanotechnology.

J. Phys. Chem. C 2014

Photoassociation of ultracold long-range polyatomic molecules

Marko Gacesa, Jason N. Byrd, Jonathan Smucker, John A. Montgomery, Jr., Robin Côté

We explore the feasibility of optically forming long-range tetratomic and larger polyatomic molecules in their ground electronic state from ultracold pairs of polar molecules aligned by external fields. Depending on the relative orientation of the interacting diatomic molecules, we find that a tetratomic can be formed either as a weakly bound complex in a very extended halo state or as a pure long-range molecule composed of collinear or nearly-collinear diatomic molecules. The latter is a novel type of tetratomic molecule comprised of two diatomic molecules bound at long intermolecular range and predicted to be stable in cold and ultracold regimes. Our numerical studies were conducted for ultracold KRb and RbCs, resulting in production of (KRb)$_2$ and (RbCs)$_2$ complexes, respectively. Based on universal properties of long-range interactions between polar molecules, we identify triatomic and tetratomic linear polar molecules with favorable ratio of dipole and quadrupole moments for which the apporach could be generalized to form polyatomic molecules.

Phys. Rev. Research 3, 023163 (2021)

10.1103/PhysRevResearch.3.023163

Chaotic internal dynamics of dissipative optical soliton molecules

Youjian Song, Defeng Zou, Omri Gat, Minglie Hu, Philippe Grelu

When a laser cavity supports the propagation of several ultrashort pulses, these pulses interact and can form compact bound states called soliton molecules. Soliton molecules are fascinating objects of nonlinear science, which present striking analogies with their matter molecules counterparts. The soliton pair, composed of two identical pulses, constitutes the chief soliton molecule of fundamental interest. The relative timing and phase between the two propagating pulses are the most salient internal degrees of freedom of the soliton molecule. These two internal degrees of freedom allow self-oscillating soliton molecules, which have indeed been repeatedly observed, whereas the lowdimensional chaotic dynamics of a soliton-pair molecule remains elusive, noting that it would require at least three degrees of freedom. We here report the observation of chaotic soliton-pair molecules within an ultrafast fiber laser, by means of a direct measurement of the relative optical pulse separation with sub-femtosecond precision in real time. Moreover, we demonstrate an all-optical control of the chaotic dynamics followed by the soliton molecule, by injecting a modulated optical signal that resynchronizes the internal periodic vibration of soliton molecule.

Driving current through single organic molecules

J. Reichert, R. Ochs, D. Beckmann, H. B. Weber, M. Mayor, H. v. Loehneysen

We investigate electronic transport through two types of conjugated molecules. Mechanically controlled break-junctions are used to couple thiol endgroups of single molecules to two gold electrodes. Current-voltage characteristics (IVs) of the metal-molecule-metal system are observed. These IVs reproduce the spatial symmetry of the molecules with respect to the direction of current flow. We hereby unambigously detect an intrinsic property of the molecule, and are able to distinguish the influence of both the molecule and the contact to the metal electrodes on the transport properties of the compound system.

Phys. Rev. Lett. 88, 176804 (2002)

10.1103/PhysRevLett.88.176804

Collisional decay of 87Rb Feshbach molecules at 1005.8 G

N. Syassen, T. Volz, S. Teichmann, S. Dürr, G. Rempe

We present measurements of the loss-rate coefficients K_am and K_mm caused by inelastic atom-molecule and molecule-molecule collisions. A thermal cloud of atomic 87Rb is prepared in an optical dipole trap. A magnetic field is ramped across the Feshbach resonance at 1007.4 G. This associates atom pairs to molecules. A measurement of the molecule loss at 1005.8 G yields K_am=2 10^-10 cm^3/s. Additionally, the atoms can be removed with blast light. In this case, the measured molecule loss yields K_mm=3 10^-10 cm^3/s.

Phys. Rev. A 74, 062706 (2006)

10.1103/PhysRevA.74.062706

Ultracold Feshbach Molecules

Francesca Ferlaino, Steven Knoop, Rudolf Grimm

In this Chapter, we give an introduction into experiments with Feshbach molecules and their applications. In particular, we discuss the various creation and detection methods, and the internal-state manipulation of such molecules. We highlight two topics, namely Feshbach molecules in the halo regime and the application of Feshbach molecule to achieve ultracold gases of molecules in the rovibrational ground state. Our illustrative examples are mainly based on work performed at Innsbruck University.

Collisions of bosonic ultracold polar molecules in microwave traps

Alexander V. Avdeenkov

The collisions between linear polar molecules, trapped in a microwave field with circular polarization, are theoretically analyzed. The microwave trap suggested by DeMille \cite{DeMille} seems to be rather advantageous in comparison with other traps. Here we have demonstrated that the microwave trap can provide a successful evaporative cooling for polar molecules in a rather broad range of frequencies of the AC-field. We suggested that not only ground state polar molecules but also molecules in some other states can be safely trapped. But the state in which molecules can be safely loaded and trapped depends on the frequency of the AC-field.

10.1088/1367-2630/11/5/055016

Formation and interactions of cold and ultracold molecules: new challenges for interdisciplinary physics

Olivier Dulieu, Carlo Gabbanini

Progress on researches in the field of molecules at cold and ultracold temperatures is reported in this review. It covers extensively the experimental methods to produce, detect and characterize cold and ultracold molecules including association of ultracold atoms, deceleration by external fields and kinematic cooling. Confinement of molecules in different kinds of traps is also discussed. The basic theoretical issues related to the knowledge of the molecular structure, the atom-molecule and molecule-molecule mutual interactions, and to their possible manipulation and control with external fields, are reviewed. A short discussion on the broad area of applications completes the review.

10.1088/0034-4885/72/8/086401

Infrared Spectra of Dehydrogenated Carbon Molecules

S. Kuzmin, W. W. Duley

The detection of fullerene molecules in a variety of astrophysical environments suggests that smaller dehydrogenated carbon molecules may also be present in these sources. One of these is planar C24 which has been shown to be more stable than the cage fullerene with the same number of carbon atoms. To facilitate searches for C24 and some simple derivatives we have calculated infrared spectra for these molecules using first principles density functional techniques (DFT). Infrared spectra are also presented for several novel carbon cage molecules formed from dehydrogenated polycyclic aromatic hydrocarbon molecules. Infrared spectra of a number of these molecules are quite distinctive and we discuss the possibility of detecting these species in the presence of C60 and other fullerenes.

Dipole Interaction Mediated Laser Cooling of Polar Molecules to Ultra-cold Temperatures

Sebastian D. Huber, Hans Peter Büchler

We present a method to design a finite decay rate for excited rotational states in polar molecules. The setup is based on a hybrid system of polar molecules with atoms driven into a Rydberg state. The atoms and molecules are coupled via the strong dipolar exchange interaction between two rotation levels of the polar molecule and two Rydberg states. Such a controllable decay rate opens the way to optically pump the hyperfine levels of polar molecules and it enables the application of conventional laser cooling techniques for cooling polar molecules into quantum degeneracy.

Phys. Rev. Lett, 108 193006 (2012)

10.1103/PhysRevLett.108.193006

An Optical Tweezer Array of Ultracold Molecules

Loïc Anderegg, Lawrence W. Cheuk, Yicheng Bao, Sean Burchesky, Wolfgang Ketterle, Kang-Kuen Ni, John M. Doyle

Arrays of single ultracold molecules promise to be a powerful platform for many applications ranging from quantum simulation to precision measurement. Here we report on the creation of an optical tweezer array of single ultracold CaF molecules. By utilizing light-induced collisions during the laser cooling process, we trap single molecules. The high densities attained inside the tweezer traps have also enabled us to observe in the absence of light molecule-molecule collisions of laser cooled molecules for the first time.

10.1126/science.aax1265

The Behavior of Benzene Confined in Single Wall Carbon Nanotube

Yu. D. Fomin, E. N. Tsiok, V. N. Ryzhov

We present the molecular dynamics study of benzene molecules confined into the single wall carbon nanotube. The local structure and orientational ordering of benzene molecules are investigated. It is found that the molecules mostly group in the middle distance from the axe of the tube to the wall. The molecules located in the vicinity of the wall demonstrate some deviation from planar shape. There is a tilted orientational ordering of the molecules which depends on the location of the molecule. It is shown that the diffusion coefficient of the benzene molecules is very small at the conditions we report here.

Contribution of internal degree of freedom of soft molecules to Soret effect

Takeaki Araki, Chikakiyo Natsumi

We studied the Soret effect in binary dimer-monomer mixtures using non-equilibrium molecular dynamics simulations and investigated the pure contribution of the internal degree of freedom of flexible molecules to the Soret effect. We observed that the thermal diffusion factor tends to decrease and change its sign as the molecules become softer. We proposed two possible mechanisms of our observations: change of the molecule structures with the temperature, causing bulkier molecules to migrate to the hotter region; asymmetry of the restitution between rigid and flexible molecules, due to which flexible molecules show larger restitution when placed at the hotter region.

Phys. Rev. E 103, 042611 (2021)

10.1103/PhysRevE.103.042611

Modeling pre-biotic self-organization: The chemical dynamics of autocatalytic networks

Varun Giri

In this thesis we present a mathematical model describing the population dynamics of molecules in an artificial chemistry where large molecules can be produced by successive ligation of pairs of smaller molecules. The chemistry contains a large number of spontaneous reactions of which a small subset could be catalyzed by molecules produced in the chemistry with varying catalytic strengths. We show ACSs, if present in the catalytic network, can focus the resources of the system into a sparse set of molecules. ACSs can produce a bistability in the population dynamics and, in particular, steady states wherein the ACS molecules dominate the population, i.e., have higher concentrations compared to the rest of molecules in the chemistry (background). In this thesis we attempt to address two main questions: First, under what circumstances do molecules belonging to the ACSs dominate over the background, and second, starting from an initial condition that does not contain good catalysts, can a sparse set of large molecules (containing several tens or a few hundred monomers) that are good catalysts arise and be maintained in the system at concentrations significantly above the background? We show that if an ACS catalyzed by large molecules contains within it (or partially overlaps with) a smaller ACS catalyzed by smaller molecules (referred to as a `nested ACS' structure), the catalytic strength required for the large ACS to dominate comes down significantly. We show that when the network contains a cascade of nested ACSs with the catalytic strengths of molecules increasing gradually with their size, a sparse subset of molecules including some very large molecules can come to dominate the system.

Molecule-molecule and atom-molecule collisions with ultracold RbCs molecules

Philip D. Gregory, Jacob A. Blackmore, Matthew D. Frye, Luke M. Fernley, Sarah L. Bromley, Jeremy M. Hutson, Simon L. Cornish

Understanding ultracold collisions involving molecules is of fundamental importance for current experiments, where inelastic collisions typically limit the lifetime of molecular ensembles in optical traps. Here we present a broad study of optically trapped ultracold RbCs molecules in collisions with one another, in reactive collisions with Rb atoms, and in nonreactive collisions with Cs atoms. For experiments with RbCs alone, we show that by modulating the intensity of the optical trap, such that the molecules spend 75% of each modulation cycle in the dark, we partially suppress collisional loss of the molecules. This is evidence for optical excitation of molecule pairs mediated via sticky collisions. We find that the suppression is less effective for molecules not prepared in the spin-stretched hyperfine ground state. This may be due either to longer lifetimes for complexes or to laser-free decay pathways. For atom-molecule mixtures, RbCs+Rb and RbCs+Cs, we demonstrate that the rate of collisional loss of molecules scales linearly with the density of atoms. This indicates that, in both cases, the loss of molecules is rate-limited by two-body atom-molecule processes. For both mixtures, we measure loss rates that are below the thermally averaged universal limit.

10.1088/1367-2630/ac3c63

Orbital hybridization and electrostatic interaction in a double molecule transistor

Xiao Guo, Qing Yang, Wei Yu, Qiuhao Zhu, Yuwen Cai, Wengang Lu, Sheng Meng, Wenjie Liang

Understanding the intermolecular interactions and utilize these interactions to effectively control the transport behavior of single molecule is the key step from single molecule device to molecular circuits1-6. Although many single molecule detection techniques are used to detect the molecular interaction at single-molecule level1,4,5,7,8, probing and tuning the intermolecular interaction all by electrical approaches has not been demonstrated. In this work, we successful assemble a double molecule transistor incorporating two manganese phthalocyanine molecules, on which we probe and tune the interaction in situ by implementing electrical manipulation on molecular orbitals using gate voltage. Orbital levels of the two molecules couple to each other and couple to the universal gate differently. Electrostatic interaction is observed when single electron changing in one molecule alters the transport behavior of the other, providing the information about the dynamic process of electron sequent tunneling through a molecule. Orbital hybridization is found when two orbital levels are put into degeneracy under non-equilibrium condition, making the tunneling electrons no longer localized to a specific molecule but shared by two molecules, offering a new mechanism to control charge transfer between non-covalent molecules. Current work offer a forelook into working principles of functional electrical unit based on single molecules.

Cold collisions of complex polyatomic molecules

Zhiying Li, Eric J. Heller

We introduce a method for classical trajectory calculations to simulate collisions between atoms and large rigid asymmetric-top molecules. Using this method, we investigate the formation of molecule-helium complexes in buffer-gas cooling experiments at a temperature of 6.5 K for molecules as large as naphthalene. Our calculations show that the mean lifetime of the naphthalene-helium quasi-bound collision complex is not long enough for the formation of stable clusters under the experimental conditions. Our results suggest that it may be possible to improve the efficiency of the production of cold molecules in buffer-gas cooling experiments by increasing the density of helium. In addition, we find that the shape of molecules is important for the collision dynamics when the vibrational motion of molecules is frozen. For some molecules, it is even more crucial than the number of accessible degrees of freedom. This indicates that by selecting molecules with suitable shape for buffer-gas cooling, it may be possible to cool molecules with a very large number of degrees of freedom.

10.1063/1.3682982

A Model to Search for Synthesizable Molecules

John Bradshaw, Brooks Paige, Matt J. Kusner, Marwin H. S. Segler, José Miguel Hernández-Lobato

Deep generative models are able to suggest new organic molecules by generating strings, trees, and graphs representing their structure. While such models allow one to generate molecules with desirable properties, they give no guarantees that the molecules can actually be synthesized in practice. We propose a new molecule generation model, mirroring a more realistic real-world process, where (a) reactants are selected, and (b) combined to form more complex molecules. More specifically, our generative model proposes a bag of initial reactants (selected from a pool of commercially-available molecules) and uses a reaction model to predict how they react together to generate new molecules. We first show that the model can generate diverse, valid and unique molecules due to the useful inductive biases of modeling reactions. Furthermore, our model allows chemists to interrogate not only the properties of the generated molecules but also the feasibility of the synthesis routes. We conclude by using our model to solve retrosynthesis problems, predicting a set of reactants that can produce a target product.

Goal directed molecule generation using Monte Carlo Tree Search

Anand A. Rajasekar, Karthik Raman, Balaraman Ravindran

One challenging and essential task in biochemistry is the generation of novel molecules with desired properties. Novel molecule generation remains a challenge since the molecule space is difficult to navigate through, and the generated molecules should obey the rules of chemical valency. Through this work, we propose a novel method, which we call unitMCTS, to perform molecule generation by making a unit change to the molecule at every step using Monte Carlo Tree Search. We show that this method outperforms the recently published techniques on benchmark molecular optimization tasks such as QED and penalized logP. We also demonstrate the usefulness of this method in improving molecule properties while being similar to the starting molecule. Given that there is no learning involved, our method finds desired molecules within a shorter amount of time.

Sampling the proteome by emerging single-molecule and mass-spectrometry methods

Michael J. MacCoss, Javier Alfaro, Meni Wanunu, Danielle A. Faivre, Nikolai Slavov

Mammalian cells have about 30,000-fold more protein molecules than mRNA molecules. This larger number of molecules and the associated larger dynamic range have major implications in the development of proteomics technologies. We examine these implications for both liquid chromatography-tandem mass spectrometry (LC-MS/MS) and single-molecule counting and provide estimates on how many molecules are routinely measured in proteomics experiments by LC-MS/MS. We review strategies that have been helpful for counting billions of protein molecules by LC-MS/MS and suggest that these strategies can benefit single-molecule methods, especially in mitigating the challenges of the wide dynamic range of the proteome. We also examine the theoretical possibilities for scaling up single-molecule and mass spectrometry proteomics approaches to quantifying the billions of protein molecules that make up the proteomes of our cells.

Nat Methods 20, 339--346 (2023)

10.1038/s41592-023-01802-5

DNA entropic elasticity for short molecules attached to beads

Jinyu Li, Philip C. Nelson, M. D. Betterton

Single-molecule experiments in which force is applied to DNA or RNA molecules have enabled important discoveries of nucleic acid properties and nucleic acid-enzyme interactions. These experiments rely on a model of the polymer force-extension behavior to calibrate the experiments; typically the experiments use the worm-like chain (WLC) theory for double-stranded DNA and RNA. This theory agrees well with experiments for long molecules. Recent single-molecule experiments have used shorter molecules, with contour lengths in the range of 1-10 persistence lengths. Most WLC theory calculations to date have assumed infinite molecule lengths, and do not agree well with experiments on shorter chains. Key physical effects that become important when shorter molecules are used include (i) boundary conditions which constrain the allowed fluctuations at the ends of the molecule and (ii) rotational fluctuations of the bead to which the polymer is attached, which change the apparent extension of the molecule. We describe the finite worm-like chain (FWLC) theory, which takes into account these effects. We show the FWLC predictions diverge from the classic WLC solution for molecules with contour lengths a few times the persistence length. Thus the FWLC will allow more accurate experimental calibration for relatively short molecules, facilitating future discoveries in single-molecule force microscopy.

Magnetic field modification of ultracold molecule-molecule collisions

T. V. Tscherbul, Yu. V. Suleimanov, V. Aquilanti, R. V. Krems

We present an accurate quantum mechanical study of molecule-molecule collisions in the presence of a magnetic field. The work focusses on the analysis of elastic scattering and spin relaxation in collisions of O2(3Sigma_g) molecules at cold (~0.1 K) and ultracold (~10^{-6} K) temperatures. Our calculations show that magnetic spin relaxation in molecule-molecule collisions is extremely efficient except at magnetic fields below 1 mT. The rate constant for spin relaxation at T=0.1 K and a magnetic field of 0.1 T is found to be as large as 6.1 x 10^{-11} cm3/s. The magnetic field dependence of elastic and inelastic scattering cross sections at ultracold temperatures is dominated by a manifold of Feshbach resonances with the density of ~100 resonances per Tesla for collisions of molecules in the absolute ground state. This suggests that the scattering length of ultracold molecules in the absolute ground state can be effectively tuned in a very wide range of magnetic fields. Our calculations demonstrate that the number and properties of the magnetic Feshbach resonances are dramatically different for molecules in the absolute ground and excited spin states. The density of Feshbach resonances for molecule-molecule scattering in the low-field-seeking Zeeman state is reduced by a factor of 10.

New J. Phys. 11, 055021 (2009)

10.1088/1367-2630/11/5/055021

Detecting high density ultracold molecules using atom-molecule collision

Jun-Ren Chen, Cheng-Yang Kao, Hung-Bin Chen, Yi-Wei Liu

Utilizing single-photon photoassociation, we have achieved ultracold rubidium molecules with a high number density that provides a new efficient approach toward molecular quantum degeneracy. A new detection mechanism for ultracold molecule utilizing the inelastic atom-molecule collision is demonstrated. The resonant coupling effect on the formation of the ${\rm X^1\Sigma^+_g}$ ground state ${\rm ^{85}Rb_2}$ allows for a sufficient number of more deeply bound ultracold molecules, which induced an additional trap loss and heating of the co-existing atoms owing to the inelastic atom-molecule collision. Therefore, after photoassociation process, the ultracold molecules can be investigated using the absorption image of the ultracold rubidium atoms mixed with the molecules in a crossed optical dipole trap. The existence of the ultracold molecules was then verified, and the amount of the accumulated molecules was measured. This method is to detect the final produced ultracold molecules, and hence distinct from the conventional trap loss experiments, which is used to study the association resonance. It is composed of measurements of the time evolution of atomic cloud and a decay model, by which the number density of the ultracold ${\rm ^{85}Rb_2}$ molecules in the optical trap was estimated to be ${\rm > 5.2\times10^{11} cm^{-3}}$.

10.1088/1367-2630/15/4/043035

Comparison of tunneling through molecules with Mott-Hubbard and with dimerization gaps

Julien Favand, Frederic Mila

In order to study the tunneling of electrons through an interacting, 1D, dimerized molecule connected to leads, we consider the persistent current in a ring embedding this molecule. We find numerically that, for spinless fermions, a molecule with a gap mostly due to interactions, i.e. a Mott-Hubbard gap, gives rise to a larger persistent current than a molecule with the same gap, but due only to the dimerization. In both cases, the tunneling current decreases exponentially with the size of the molecule, but more slowly in the interacting case. Implications for molecular electronic are briefly discussed.

10.1007/s100510050252

Observation of Feshbach-like resonances in collisions between ultracold molecules

C. Chin, T. Kraemer, M. Mark, J. Herbig, P. Waldburger, H. -C. Naegerl, R. Grimm

We observe magnetically tuned collision resonances for ultracold Cs2 molecules stored in a CO2-laser trap. By magnetically levitating the molecules against gravity, we precisely measure their magnetic moment. We find an avoided level crossing which allows us to transfer the molecules into another state. In the new state, two Feshbach-like collision resonances show up as strong inelastic loss features. We interpret these resonances as being induced by Cs4 bound states near the molecular scattering continuum. The tunability of the interactions between molecules opens up novel applications such as controlled chemical reactions and synthesis of ultracold complex molecules.

Phys.Rev.Lett.94:123201,2005

10.1103/PhysRevLett.94.123201

Ultracold heteronuclear molecules in a 3D optical lattice

C. Ospelkaus, S. Ospelkaus, L. Humbert, P. Ernst, K. Sengstock, K. Bongs

We report on the creation of ultracold heteronuclear molecules assembled from fermionic 40K and bosonic 87Rb atoms in a 3D optical lattice. Molecules are produced at a heteronuclear Feshbach resonance both on the attractive and the repulsive side of the resonance. We precisely determine the binding energy of the heteronuclear molecules from rf spectroscopy across the Feshbach resonance. We characterize the lifetime of the molecular sample as a function of magnetic field and measure between 20 and 120ms. The efficiency of molecule creation via rf association is measured and is found to decrease as expected for more deeply bound molecules.

Phys. Rev. Lett. 97, 120402 (2006)

10.1103/PhysRevLett.97.120402

Non-Local Conductance Modulation by Molecules: STM of Substituted Styrene Heterostructures on H-Terminated Si(100)

Paul G. Piva, Robert A. Wolkow, George Kirczenow

One-dimensional organic heterostructures consisting of contiguous lines of CF3- and OCH3-substituted styrene molecules on silicon are studied by scanning tunneling microscopy and ab initio simulation. Dipole fields of OCH3-styrene molecules are found to enhance conduction through molecules near OCH3-styrene/CF3-styrene heterojunctions. Those of CF3-styrene depress transport through the nearby silicon. Thus choice of substituents and their attachment site on host molecules provide a means of differentially tuning molecule and substrate transport at the molecular scale.

10.1103/PhysRevLett.101.106801

Ultracold Heteronuclear Fermi-Fermi Molecules

A. -C. Voigt, M. Taglieber, L. Costa, T. Aoki, W. Wieser, T. W. Hänsch, K. Dieckmann

We report on the first creation of ultracold bosonic heteronuclear molecules of two fermionic species, 6Li and 40K, by a magnetic field sweep across an interspecies s-wave Feshbach resonance. This allows us to associate up to 4x10^4 molecules with high efficiencies of up to 50%. Using direct imaging of the molecules, we measure increased lifetimes of the molecules close to resonance of more than 100 ms in the molecule-atom mixture stored in a harmonic trap.

10.1103/PhysRevLett.102.020405

Dissociative Electron Attachment to Polyatomic Molecules - V : Formic Acid and Propyl Amine

N. Bhargava Ram, E. Krishnakumar

In this paper, we discuss the dissociative electron attachment process in Formic Acid and Propyl Amine. These are molecules containing more than one functional group and have low symmetry (Cs group). We measured the kinetic energy and angular distributions of fragment H^{-} ions from the resonances observed in these molecules and compared with that in the precursor molecules, namely - Water, Ammonia and Methane. Measurements suggest that the dissociation dynamics in bigger molecules are independent of overall symmetry of the molecule, rather depend only on the local symmetry of functional group and bond orientation factors.

Single-molecule interfacial electron transfer dynamics manipulated by external electric current

Guofeng Zhang, Liantuan Xiao, Ruiyun Chen, Yan Gao, Xiaobo Wang, Suotang Jia

Interfacial electron transfer (IET) dynamics in 1,1'-dioctadecyl-3, 3, 3', 3'-tetramethylindodicarbocyanine (DiD) dye molecules / indium tin oxide (ITO) film system have been probed at the ensemble and single-molecule level by recording the change of fluorescence emission intensity. By comparing the difference of the external electric current (EEC) dependence of lifetime and intensity for enambles and single molecules, it is shown that the single-molecule probe can effcienly demonstrate the IET dynamics. The backward electron transfer and electron transfer of ground state induce the single molecules fluorescence quenching when an EEC is applied to ITO film.

10.1039/C1CP20857H

Controllable binding of polar molecules and meta-stability of 1-D gases with attractive dipole forces

Jason N. Byrd, John A. Montgomery Jr, Robin Côté

We explore one-dimensional (1-D) samples of ultracold polar molecules with attractive dipole-dipole interactions and show the existence of a repulsive barrier due to a strong quadrupole interaction between molecules. This barrier can stabilize a gas of ultracold KRb molecules and even lead to long-range wells supporting bound states between molecules. The properties of these wells can be controlled by external electric fields, allowing the formation of long polymer-like chains of KRb, and studies of quantum phase transitions by varying the effective interaction between molecules. We discuss the generalization of those results to other systems.

10.1103/PhysRevLett.109.083003

Blinking Molecule Tracking

Andreas Karrenbauer, Dominik Wöll

We discuss a method for tracking individual molecules which globally optimizes the likelihood of the connections between molecule positions fast and with high reliability even for high spot densities and blinking molecules. Our method works with cost functions which can be freely chosen to combine costs for distances between spots in space and time and which can account for the reliability of positioning a molecule. To this end, we describe a top-down polyhedral approach to the problem of tracking many individual molecules. This immediately yields an effective implementation using standard linear programming solvers. Our method can be applied to 2D and 3D tracking.

A proposal for sympathetically cooling neutral molecules using cold ions

F. Robicheaux

We describe a method for cooling neutral molecules that have magnetic and electric dipole moments using collisions with cold ions. An external magnetic field is used to split the ground rovibrational energy levels of the molecule. The highest energy state within the ground rovibrational manifold increases in energy as the distance to the ion decreases leading to a repelling potential. At low energy, inelastic collisions are strongly suppressed due to the large distance of closest approach. Thus, a collision between a neutral molecule and a cold ion will lead to a decrease in the molecule's kinetic energy with no change in internal energy. We present results for the specific case of OH molecules cooled by Be$^+$, Mg$^+$, or Ca$^+$ ions.

Phys. Rev. A 89, 062701 (2014)

10.1103/PhysRevA.89.062701

Adiabatic field-free alignment of asymmetric top molecules with an optical centrifuge

A. Korobenko, V. Milner

We use an optical centrifuge to align asymmetric top $\mathrm{SO_2}$ molecules by adiabatically spinning their most polarizable O-O axis. The effective centrifugal potential in the rotating frame confines sulfur atoms to the plane of the laser-induced rotation, leading to the planar molecular alignment which persists after the molecules are released from the centrifuge. Periodic appearance of the full three-dimensional alignment, typically observed only with linear and symmetric top molecules, is also detected. Together with strong in-plane centrifugal forces, which bend the molecules by up to 10 degrees, permanent field-free alignment offers new ways of controlling molecules with laser light.

Phys. Rev. Lett. 116, 183001 (2016)

10.1103/PhysRevLett.116.183001

Improved spatial separation of neutral molecules

Jens S. Kienitz, Karol Długołecki, Sebastian Trippel, Jochen Küpper

We have developed and experimentally demonstrated an improved electrostatic deflector for the spatial separation of molecules according to their dipole-moment-to-mass ratio. The device features a very open structure that allows for significantly stronger electric fields as well as for stronger deflection without molecules crashing into the device itself. We have demonstrated its performance using the prototypical OCS molecule and we discuss opportunities regarding improved quantum-state-selectivity for complex molecules and the deflection of unpolar molecules.

J. Chem. Phys. 147, (2017)

10.1063/1.4991479

Rotational States of Magnetic Molecules

E. M. Chudnovsky, D. A. Garanin

We study a magnetic molecule that exhibits spin tunneling and is free to rotate about its anisotropy axis. Exact low-energy eigenstates of the molecule that are superpositions of spin and rotational states are obtained. We show that parameter $\alpha = 2(\hbar S)^2/(I\Delta)$ determines the ground state of the molecule. Here $\hbar S$ is the spin, $I$ is the moment of inertia, and $\Delta$ is the tunnel splitting. The magnetic moment of the molecule is zero at $\alpha < \alpha_c = [1-1/(2S)^{2}]^{-1}$ and non-zero at $\alpha > \alpha_c$. At $\alpha \to \infty$ the spin of the molecule localizes in one of the directions along the anisotropy axis.

Physical Review B 81, 214423 (2010) [5 pages]

10.1103/PhysRevB.81.214423

Vibrational energy transfer in ultracold molecule - molecule collisions

Goulven Quéméner, Naduvalath Balakrishnan, Roman V. Krems

We present a rigorous study of vibrational relaxation in p-H2 + p-H2 collisions at cold and ultracold temperatures and identify an efficient mechanism of ro-vibrational energy transfer. If the colliding molecules are in different rotational and vibrational levels, the internal energy may be transferred between the molecules through an extremely state-selective process involving simultaneous conservation of internal energy and total rotational angular momentum. The same transition in collisions of distinguishable molecules corresponds to the rotational energy transfer from one vibrational state of the colliding molecules to another.

Phys. Rev. A 77, 030704(R) (2008)

10.1103/PhysRevA.77.030704

Nondestructive Detection of Polar Molecules via Rydberg Atoms

Martin Zeppenfeld

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.

Europhys. Lett. 118 13002 (2017)

10.1209/0295-5075/118/13002

Active Colloidal Molecules

Hartmut Löwen

Like ordinary molecules are composed of atoms, colloidal molecules consist of several species of colloidal particles tightly bound together. If one of these components is self-propelled or swimming, novel "active colloidal molecules" emerge. Active colloidal molecules exist on various levels such as "homonuclear", "heteronuclear" and "polymeric" and possess a dynamical function moving as propellers, spinners or rotors. Self-assembly of such active complexes has been studied a lot recently and this perspective article summarizes recent progress and gives an outlook to future developments in the rapidly expanding field of active colloidal molecules.

EPL 121, 58001 (2018)

10.1209/0295-5075/121/58001

Quantum Zeno-based Detection and State Engineering of Ultracold Polar Molecules

Amit Jamadagni, Silke Ospelkaus, Luis Santos, Hendrik Weimer

We present and analyze a toolbox for the controlled manipulation of ultracold polar molecules, consisting of detection of molecules, atom-molecule entanglement, and engineering of dissipative dynamics. Our setup is based on fast chemical reactions between molecules and atoms leading to a quantum Zeno-based collisional blockade in the system. We demonstrate that the experimental parameters for achieving high fidelities can be found using a straightforward numerical optimization. We exemplify our approach for a system comprised of NaK molecules and Na atoms and we discuss the consequences of residual imperfections such as a finite strength of the quantum Zeno blockade.

Phys. Rev. Research 3, 033208 (2021)

10.1103/PhysRevResearch.3.033208

A general Zeeman slower for type-II transitions and polar molecules

Qian Liang, Wenhao Bu, Yuhe Zhang, Tao Chen, Bo Yan

We proposed a general Zeeman slower scheme applicable to the majority of the laser-coolable molecules. Different from previous schemes, the key idea of our scheme lies in that the compensation of the detuning with the magnetic field is done for the repumping laser instead of the cooling laser. Only atoms or molecules with the right velocity will be repumped and laser slowed. Such scheme is more feasible for molecules with complex energy sturcutres. We apply this scheme for molecules with large Land\'e g-factor of the excited states and polyatomic molecules, and it shows a better slowing efficiency.

Phys. Rev. A 100, 053402 (2019)

10.1103/PhysRevA.100.053402

Single Molecule Mixture: A Concept in Polymer Science

Yu Tang

In theory, there exist two extreme forms of substances: pure form and single-molecule mixture form. Single-molecule mixture form contains a mixture of molecules that have molecularly different structures. This elusive form has not yet been explored. Herein, we report a study of single molecule mixture state by a combination of model construction and mathematical analysis, and a series of interesting results were obtained. These results provide theoretical evidence that single-molecule mixture state may indeed exist in realistic synthetic or natural polymer system.

BaF molecules in neon ice: trapping, spectroscopy and optical control of electron spins

Samuel J. Li, Harish D. Ramachandran, Rhys Anderson, Amar C. Vutha

We have trapped BaF molecules in neon ice, and used laser-induced fluorescence spectroscopy to map out optical transitions in the trapped molecules. Our measurements show that the neon lattice does not significantly perturb certain optical transitions in the trapped molecules. We used one of these transitions to polarize the electron spins, detect spin flips and measure hyperfine transitions in the trapped molecules, entirely using lasers. This demonstration with heavy polar molecules opens up new opportunities for precision measurements of beyond-standard-model physics.

Two-probe theory of scanning tunneling microscopy of single molecules: Zn(II)-etioporphyrin on alumina

John Buker, George Kirczenow

We explore theoretically the scanning tunneling microscopy of single molecules on substrates using a framework of two local probes. This framework is appropriate for studying electron flow in tip/molecule/substrate systems where a thin insulating layer between the molecule and a conducting substrate transmits electrons non-uniformly and thus confines electron transmission between the molecule and substrate laterally to a nanoscale region significantly smaller in size than the molecule. The tip-molecule coupling and molecule-substrate coupling are treated on the same footing, as local probes to the molecule, with electron flow modelled using the Lippmann-Schwinger Green function scattering technique. STM images are simulated for various positions of the stationary (substrate) probe below a Zn(II)-etioporphyrin I molecule. We find that these images have a strong dependence on the substrate probe position, indicating that electron flow can depend strongly on both tip position and the location of the dominant molecule-substrate coupling. Differences in the STM images are explained in terms of the molecular orbitals that mediate electron flow in each case. Recent experimental results, showing STM topographs of Zn(II)-etioporphyrin I on alumina/NiAl(110) to be strongly dependent on which individual molecule on the substrate is being probed, are explained using this model. A further experimental test of the model is also proposed.

10.1103/PhysRevB.72.205338

Laser cooling of a diatomic molecule

E. S. Shuman, J. F. Barry, D. DeMille

It has been roughly three decades since laser cooling techniques produced ultracold atoms, leading to rapid advances in a vast array of fields. Unfortunately laser cooling has not yet been extended to molecules because of their complex internal structure. However, this complexity makes molecules potentially useful for many applications. For example, heteronuclear molecules possess permanent electric dipole moments which lead to long-range, tunable, anisotropic dipole-dipole interactions. The combination of the dipole-dipole interaction and the precise control over molecular degrees of freedom possible at ultracold temperatures make ultracold molecules attractive candidates for use in quantum simulation of condensed matter systems and quantum computation. Also ultracold molecules may provide unique opportunities for studying chemical dynamics and for tests of fundamental symmetries. Here we experimentally demonstrate laser cooling of the molecule strontium monofluoride (SrF). Using an optical cycling scheme requiring only three lasers, we have observed both Sisyphus and Doppler cooling forces which have substantially reduced the transverse temperature of a SrF molecular beam. Currently the only technique for producing ultracold molecules is by binding together ultracold alkali atoms through Feshbach resonance or photoassociation. By contrast, different proposed applications for ultracold molecules require a variety of molecular energy-level structures. Our method provides a new route to ultracold temperatures for molecules. In particular it bridges the gap between ultracold temperatures and the ~1 K temperatures attainable with directly cooled molecules (e.g. cryogenic buffer gas cooling or decelerated supersonic beams). Ultimately our technique should enable the production of large samples of molecules at ultracold temperatures for species that are chemically distinct from bialkalis.

Nature 467, 820-823 (2010)

10.1038/nature09443

Cavity-meidated collisionless sympathetic cooling of molecules with atoms

Guangjiong Dong, Chang Wang, Weiping Zhang

Cooling a range of molecules to ultracold temperatures (<1 mK) is a difficult but important challenge in molecular physics and chemistry. Collective cavity cooling of molecules is a promising method that does not rely on molecular energy level and thus can be applied to all molecules in principle. However, the initial lack of cold molecules leads to the difficulty in its experimental implementation. We show that efficient collective sympathetic cooling of molecules to sub-mK temperatures using a large ensemble of atoms within a cavity is feasible. This approach is a new type of sympathetic cooling which does not rely on direct collisions between atoms and molecules, but utilizes thermalization via their mutual interaction with a cavity field. Two important mechanisms are identified. This include: (1) giant enhancement of cavity optical field from the efficient scattering of the pump light by the atoms; (2) cavity-mediated collective interaction between the atoms and the molecules. We show an optimal cavity detuning for maximizing cooling, which is dependent on the atom and molecule numbers. We determine a threshold for the molecular pump strength and show that it is independent of molecule number when the number of atoms is much greater than the molecules. This can be reduced by orders of magnitude when compared to cavity cooling of single molecular species only. Using this new sympathetic cavity cooling technique, cooling molecules to sub-mK within a high-Q cavity could be within reach of experimental demonstration.

Molecules associated to Hardy spaces with pointwise variable anisotropy

Víctor Almeida, Jorge J. Betancor, Lourdes Rodríguez-Mesa

In this paper we introduce molecules associated to Hardy spaces with pointwise variable anisotropy, and prove that each molecule can be represented as a sum of atoms.

Theory of chemical evolution of molecule compositions in the universe, in the Miller-Urey experiment and the mass distribution of interstellar and intergalactic molecules

Stuart A. Kauffman, David P. Jelenfi, Gabor Vattay

Chemical evolution is essential in understanding the origins of life. We present a theory for the evolution of molecule masses and show that small molecules grow by random diffusion and large molecules by a preferential attachment process leading eventually to life's molecules. It reproduces correctly the distribution of molecules found via mass spectroscopy for the Murchison meteorite and estimates the start of chemical evolution back to 12.8 billion years following the birth of stars and supernovae. From the Frontier mass between the random and preferential attachment dynamics the birth time of molecule families can be estimated. Amino acids emerge about 165 million years after chemical elements emerge in stars. Using the scaling of reaction rates with the distance of the molecules in space we recover correctly the few days emergence time of amino acids in the Miller-Urey experiment. The distribution of interstellar and extragalactic molecules are both consistent with the evolutionary mass distribution, and their age is estimated to 108 and 65 million years after the start of evolution. From the model, we can determine the number of different molecule compositions at the time of the emergence of Earth to be 1.6 million and the number of molecule compositions in interstellar space to a mere 719 species.

Journal of Theoretical Biology 2019

MIMOSA: Multi-constraint Molecule Sampling for Molecule Optimization

Tianfan Fu, Cao Xiao, Xinhao Li, Lucas M. Glass, Jimeng Sun

Molecule optimization is a fundamental task for accelerating drug discovery, with the goal of generating new valid molecules that maximize multiple drug properties while maintaining similarity to the input molecule. Existing generative models and reinforcement learning approaches made initial success, but still face difficulties in simultaneously optimizing multiple drug properties. To address such challenges, we propose the MultI-constraint MOlecule SAmpling (MIMOSA) approach, a sampling framework to use input molecule as an initial guess and sample molecules from the target distribution. MIMOSA first pretrains two property agnostic graph neural networks (GNNs) for molecule topology and substructure-type prediction, where a substructure can be either atom or single ring. For each iteration, MIMOSA uses the GNNs' prediction and employs three basic substructure operations (add, replace, delete) to generate new molecules and associated weights. The weights can encode multiple constraints including similarity and drug property constraints, upon which we select promising molecules for next iteration. MIMOSA enables flexible encoding of multiple property- and similarity-constraints and can efficiently generate new molecules that satisfy various property constraints and achieved up to 49.6% relative improvement over the best baseline in terms of success rate. The code repository (including readme file, data preprocessing and model construction, evaluation) is available https://github.com/futianfan/MIMOSA.

Growth modes of partially fluorinated organic molecules on amorphous silicon dioxide

Mila Miletic, Karol Palczynski, Joachim Dzubiella

We study the influence of fluorination on nucleation and growth of the organic para-sexiphenyl molecule (p-6P) on amorphous silicon dioxide ($\alpha$-SiO$_2$) by means of atomistically resolved classical molecular dynamics computer simulations. We use a simulation model that mimics the experimental deposition from the vapor and subsequent self-assembly onto the underlying surface. Our model reproduces the experimentally observed orientational changes from lying to upright standing configurations of the grown layers. We demonstrate that the increase in the number of fluorinated groups inside the p-6P leads to a smoother, layer-by-layer growth on the $\alpha$-SiO$_2$ surface: We observe that in the first layers, due to strong molecule-substrate interactions the molecules first grow in chiral (fan-like) structures, where each consecutive molecule has a higher angle, supported by molecules lying underneath. Subsequently deposited molecules bind to the already standing molecules of the chiral structures until all molecules are standing. The growth of chiral islands is the main mechanism for growth of the fluorinated p-6P derivative, while the p-6P, due to the lower interaction with the underlying substrate, forms less chiral structures. This leads to a lower energy barrier for step-edge crossing for the fluorinated molecules. We find that partial fluorination of the p-6P molecule can in this way significantly alter its growth behaviour by modifying the rough, 3D growth into a smooth, layer-by-layer growth. This has implications for the rational design of molecules and their functionalized forms which could be tailored for a desired growth behavior and structure formation.

A simple approach to the correlation of rotovibrational states in four-atomic molecules

N. Manini, S. Oss

The problem of correlation between quantum states of four-atomic molecules in different geometrical configurations is reviewed in detail. A general, still simple rule is obtained which allows one to correlate states of a linear four-atomic molecule with those of any kind of non-linear four-atomic molecule.

Z. Phys. D 32, 85 (1994)

10.1007/BF01425928

Quantum Theory of Chiral Interactions in Cholesteric Liquid Crystals

A. S. Issaenko, A. B. Harris, T. C. Lubensky

We study the effective chiral interaction between molecules arising from quantum dispersion interactions within a model in which a) the dominant excited states of a molecule form a band whose width is small compared to the average excitation energy and b) biaxial orientational correlation between adjacent molecules can be neglected. Previous treatments of quantum chiral interactions were based on a multipole expansion of the intermolecular interaction. However, because real liquid crystals are composed of elongated molecules, we utilize an expansion in terms of only coordinates transverse to the long molecular axes. We identify two distinct physical limits depending on whether one or both of the interacting molecules are excited in the virtual state. When both molecules are excited, our results are similar to those found previously by van der Meer et al. Previously unidentified terms in which only one molecule is excited involve the interactions of local dipole moments, which exist even when the global dipole moment of the molecule vanishes. We present analytic and numerical results for helical molecules. Our results do not indicate whether the dominant chiral interaction in cholesterics results from quantum or from steric interactions.

Slow Vibrations in Transport through Molecules

Tero T. Heikkila, Wolfgang Belzig

We show how one can measure the signal from slow jumps of a single molecule between metastable positions using a setup where the molecule is fixed to one lead, and one of the coupling strengths is controlled externally. Such a measurement yields information about slow processes deforming the molecule in times much longer than the characteristic time scales for the electron transport process.

Nano Lett. 5, 2088 (2005)

10.1021/nl051453a

Signatures of Molecular Magnetism in Single-Molecule Transport Spectroscopy

Moon-Ho Jo, Jacob E. Grose, Kanhayalal Baheti, Mandar M. Deshmukh, Jennifer J. Sokol, Evan M. Rumberger, David N. Hendrickson, Jeffrey R. Long, Hongkun Park, D. C. Ralph

Single-molecule transistors provide a unique experimental tool to investigate the coupling between charge transport and the molecular degrees of freedom in individual molecules. One interesting class of molecules for such experiments are the single-molecule magnets, since the intramolecular exchange forces present in these molecules should couple strongly to the spin of transport electrons, thereby providing both new mechanisms for modulating electron flow and also new means for probing nanoscale magnetic excitations. Here we report single-molecule transistor measurements on devices incorporating Mn12 molecules. By studying the electron-tunneling spectrum as a function of magnetic field, we are able to identify clear signatures of magnetic states and their associated magnetic anisotropy. A comparison of the data to simulations also suggests that electron flow can strongly enhance magnetic relaxation of the magnetic molecule.

10.1021/nl061212i

Molecular Self-Assembly of Jointed Molecules on a Metallic Substrate: From Single Molecule to Monolayer

T. Zambelli, S. Goudeau, J. Lagoute, A. Gourdon, X. Bouju, S. Gauthier

Because of its promising contribution to the bottom-up approach for nanofabrication of complex molecular architectures, self-organization is widely studied nowadays. Numerous studies have tackled supramolecular chirality or low-dimensional molecular nanostructures using in most cases small and rigid molecules adsorbed on metallic substrates. In this situation, self-assembled structures can be understood in relative simple terms considering molecule-molecule versus molecule-substrate interactions. In contrast, the case of large and three-dimensional molecules which can adopt different adsorption conformations is more complex. Here, we investigate the self-assembly of V-Landers molecules (C108H104) on Cu(100) by STM at room temperature under ultrahigh vacuum. This molecule is constituted of a central poly-aromatic board linked by sigma bonds to four 3,5-di-tert-butylphenyl legs.

Dependence of Single Molecule Junction Conductance on Molecular Conformation

Latha Venkataraman, Jennifer E. Klare, Colin Nuckolls, Mark S. Hybertsen, Michael L. Steigerwald

The conductance of a single metal-molecule-metal junction depends critically on the conformations of the molecule. In the simple case of a biphenyl, two phenyl rings linked together by a single C-C bond, the conductance is expected to depend on the relative twist angle between the two rings, with the planar conformation having the highest conductance. A number of different techniques have measured the conductance of metal-molecule(s)-metal junctions. However, the conductance variation from junction to junction has made it difficult to verify even the simplest predictions about how molecules should behave in unimolecular devices. Here, using amine link groups to form single molecule junctions, we show a clear correlation between molecule conformation and junction conductance in a series of seven biphenyl molecules with different ring substitutions that alter the twist angle of the molecules. We find that the conductance for the series decreases with increasing twist angle, consistent with a cosine squared relation predicted theoretically for transport through pi-conjugated systems.

10.1038/nature05037

Prospects for making polar molecules with microwave fields

Svetlana Kotochigova

We propose a new mechanism to produce ultracold polar molecules with microwave fields. The proposed mechanism converts trapped ultracold atoms of different species into vibrationally excited molecules by a single microwave transition and entirely depends on the existence of a permanent dipole moment in the molecules. As opposed to production of molecules by photoassociation or magnetic-field Feshbach resonances our method does not rely on the structure and lifetime of excited states or existence of Feshbach resonances. In addition, we determine conditions for optimal creation of polar molecules in vibrationally excited states of the ground-state potential by changing frequency and intensity of the microwave field. We also explore the possibility to produce vibrationally cold molecules by combining the microwave field with an optical Raman transition or by applying a microwave field to Feshbach molecules. The production mechanism is illustrated for two polar molecules: KRb and RbCs.

10.1103/PhysRevLett.99.073003

Rotation of C60 in a single-molecule contact

N. Neel, L. Limot, J. Kroeger, R. Berndt

The orientation of individual C60 molecules adsorbed on Cu(100) is reversibly switched when the tip of a scanning tunneling microscope is approached to contact the molecule. The probability of switching rises sharply upon displacing the tip beyond a threshold. A mechanical mechanism is suggested to induce the rotation of the molecule.

10.1103/PhysRevB.77.125431

Strong Correlations and Fickian Water Diffusion in Narrow Carbon Nanotubes

Biswaroop Mukherjee, Prabal K. Maiti, Chandan Dasgupta, A. K. Sood

We have used atomistic molecular dynamics (MD) simulations to study the structure and dynamics of water molecules inside an open ended carbon nanotube placed in a bath of water molecules. The size of the nanotube allows only a single file of water molecules inside the nanotube. The water molecules inside the nanotube show solid-like ordering at room temperature, which we quantify by calculating the pair correlation function. It is shown that even for the longest observation times, the mode of diffusion of the water molecules inside the nanotube is Fickian and not sub-diffusive. We also propose a one-dimensional random walk model for the diffusion of the water molecules inside the nanotube. We find good agreement between the mean-square displacements calculated from the random walk model and from MD simulations, thereby confirming that the water molecules undergo normal-mode diffusion inside the nanotube. We attribute this behavior to strong positional correlations that cause all the water molecules inside the nanotube to move collectively as a single object. The average residence time of the water molecules inside the nanotube is shown to scale quadratically with the nanotube length.

Journal of Chemical Physics, 126, 124704 (2007)

10.1063/1.2565806

Preparation and manipulation of molecules for fundamental physics tests

M. R. Tarbutt, J. J. Hudson, B. E. Sauer, E. A. Hinds

This paper is a chapter from an upcoming book on cold molecule physics. In it we describe techniques for the preparation and manipulation of cold molecules. We further describe techniques for applying said cold molecules to tests of fundamental physics.

Rydberg atom mediated polar molecule interactions: a tool for molecular-state conditional quantum gates and individual addressability

Elena Kuznetsova, Seth T. Rittenhouse, Hossein R. Sadeghpour, Susanne F. Yelin

We study the possibility to use interaction between a polar molecule in the ground electronic and vibrational state and a Rydberg atom to construct two-qubit gates between molecular qubits and to coherently control molecular states. A polar molecule within the electron orbit in a Rydberg atom can either shift the Rydberg state, or form Rydberg molecule. Both the atomic shift and the Rydberg molecule states depend on the initial internal state of the polar molecule, resulting in molecular state dependent van der Waals or dipole-dipole interaction between Rydberg atoms. Rydberg atoms mediated interaction between polar molecules can be enhanced up to $10^{3}$ times. We describe how the coupling between a polar molecule and a Rydberg atom can be applied to coherent control of molecular states, specifically, to individual addressing of molecules in an optical lattice and non-destructive readout of molecular qubits.

10.1039/C1CP21476D

The origin of large molecules in primordial autocatalytic reaction networks

Varun Giri, Sanjay Jain

Large molecules such as proteins and nucleic acids are crucial for life, yet their primordial origin remains a major puzzle. The production of large molecules, as we know it today, requires good catalysts, and the only good catalysts we know that can accomplish this task consist of large molecules. Thus the origin of large molecules is a chicken and egg problem in chemistry. Here we present a mechanism, based on autocatalytic sets (ACSs), that is a possible solution to this problem. We discuss a mathematical model describing the population dynamics of molecules in a stylized but prebiotically plausible chemistry. Large molecules can be produced in this chemistry by the coalescing of smaller ones, with the smallest molecules, the `food set', being buffered. Some of the reactions can be catalyzed by molecules within the chemistry with varying catalytic strengths. Normally the concentrations of large molecules in such a scenario are very small, diminishing exponentially with their size. ACSs, if present in the catalytic network, can focus the resources of the system into a sparse set of molecules. ACSs can produce a bistability in the population dynamics and, in particular, steady states wherein the ACS molecules dominate the population. However to reach these steady states from initial conditions that contain only the food set typically requires very large catalytic strengths, growing exponentially with the size of the catalyst molecule. We present a solution to this problem by studying `nested ACSs', a structure in which a small ACS is connected to a larger one and reinforces it. We show that when the network contains a cascade of nested ACSs with the catalytic strengths of molecules increasing gradually with their size (e.g., as a power law), a sparse subset of molecules including some very large molecules can come to dominate the system.

10.1371/journal.pone.0029546

Geometrical terms in the effective Hamiltonian for rotor molecules

Ian G. Moss

An analogy between asymmetric rotor molecules and anisotropic cosmology can be used to calculate new centrifugal distortion terms in the effective potential of asymmetric rotor molecules which have no internal 3-fold symmetry. The torsional potential picks up extra $\cos\alpha$ and $\cos2\alpha$ contributions, which are comparable to corrections to the momentum terms in methanol and other rotor molecules with isotope replacements.

Manipulation of Molecules with Electromagnetic Fields

Mikhail Lemeshko, Roman V. Krems, John M. Doyle, Sabre Kais

The goal of the present article is to review the major developments that have led to the current understanding of molecule-field interactions and experimental methods for manipulating molecules with electromagnetic fields. Molecule-field interactions are at the core of several, seemingly distinct, areas of molecular physics. This is reflected in the organization of this article, which includes sections on Field control of molecular beams, External field traps for cold molecules, Control of molecular orientation and molecular alignment, Manipulation of molecules by non-conservative forces, Ultracold molecules and ultracold chemistry, Controlled many-body phenomena, Entanglement of molecules and dipole arrays, and Stability of molecular systems in high-frequency super-intense laser fields. The article contains 853 references.

Molecular Physics 111, 1648 (2013)

10.1080/00268976.2013.813595

Formation of Ultracold NaRb Feshbach Molecules

Fudong Wang, Xiaodong He, Xiaoke Li, Bing Zhu, Jun Chen, Dajun Wang

We report the creation of ultracold bosonic $^{23}$Na$^{87}$Rb Feshbach molecules via magneto-association. By ramping the magnetic field across an interspecies Feshbach resonance, at least 4000 molecules can be produced out of the near degenerate ultracold mixture. Fast loss due to inelastic atom-molecule collisions is observed, which limits the pure molecule number, after residual atoms removal, to 1700. The pure molecule sample can live for 21.8(8) ms in the optical trap, long enough for future molecular spectroscopy studies toward coherently transferring to the singlet ro-vibrational ground state, where these molecules are stable against chemical reaction and have a permanent electric dipole moment of 3.3 Debye. We have also measured the Feshbach molecule's binding energy near the Feshbach resonance by the oscillating magnetic field method and found these molecules have a large closed-channel fraction.

New J. Phys. 17 035003(2015)

10.1088/1367-2630/17/3/035003

Generating Focussed Molecule Libraries for Drug Discovery with Recurrent Neural Networks

Marwin H. S. Segler, Thierry Kogej, Christian Tyrchan, Mark P. Waller

In de novo drug design, computational strategies are used to generate novel molecules with good affinity to the desired biological target. In this work, we show that recurrent neural networks can be trained as generative models for molecular structures, similar to statistical language models in natural language processing. We demonstrate that the properties of the generated molecules correlate very well with the properties of the molecules used to train the model. In order to enrich libraries with molecules active towards a given biological target, we propose to fine-tune the model with small sets of molecules, which are known to be active against that target. Against Staphylococcus aureus, the model reproduced 14% of 6051 hold-out test molecules that medicinal chemists designed, whereas against Plasmodium falciparum (Malaria) it reproduced 28% of 1240 test molecules. When coupled with a scoring function, our model can perform the complete de novo drug design cycle to generate large sets of novel molecules for drug discovery.

Terahertz dynamics of electron-vibron coupling in single molecules with tunable electrostatic potential

Shaoqing Du, Kenji Yoshida, Ya Zhang, Ikutaro Hamada, Kazuhiko Hirakawa

Clarifying electronic and vibronic properties at individual molecule level provides key insights to future chemistry, nanoelectronics, and quantum information technologies. The single electron tunneling spectroscopy has been used to study the charging/discharging process in single molecules. The obtained information was, however, mainly on static electronic properties, and access to their dynamical properties was very indirect. Here, we report on the terahertz (THz) spectroscopy of single fullerene molecules by using a single molecule transistor (SMT) geometry. From the time-domain THz autocorrelation measurements, we have obtained THz spectra associated with the THz-induced center-of-mass oscillation of the molecules. The observed peaks are finely split into two, reflecting the difference in the van der Waals potential profile experienced by the molecule on the metal surface when the number of electrons on the molecule fluctuates by one during the single electron tunneling process. Such an ultrahigh-sensitivity to the electronic/vibronic structures of a single molecule upon adding/removing a single electron has been achieved by using the THz spectroscopy in the SMT geometry. This novel scheme provides a new opportunity for investigating ultrafast THz dynamics of sub-nm scale systems.

10.1038/s41566-018-0241-1

Interference in Electron-Molecule Elastic Scattering: s-, p- and d-spherical waves

A. S. Baltenkov, S. T. Manson, A. Z. Msezane

General formulas describing the multiple scattering of electron by polyatomic molecules have been derived within the framework of the model of non-overlapping atomic potentials. These formulas are applied to different carbon molecules, both for fixed-in-space and randomly oriented molecules.

Simple hydrogen-bearing molecules in translucent molecular clouds

T. Weselak, J. Krełowski

We demonstrate relations between column densities of simple molecules: CH, CH$^{+}$, H$_{2}$ and OH. The H$_{2}$, CH and OH molecules seem to occupy the same environments because of tight relations between their column densities. In contrary to this CH$^{+}$ column density does not correlate with those of other simple molecules.

Faddeev Random Phase Approximation applied to molecules

Matthias Degroote

This Ph.D. thesis derives the equations of the Faddeev Random Phase Approximation (FRPA) and applies the method to a set of small atoms and molecules. The occurence of RPA instabilities in the dissociation limit is addressed in molecules and by the study of the Hubbard molecule as a test system with reduced dimensionality.

10.1140/epjst/e2013-01772-8

Inducing the controlled rotation of single o MeO DMBI molecules anchored on Au(111)

Frank Eisenhut, Jörg Meyer, Justus Krüger, Robin Ohmann, Gianaurelio Cuniberti, Francesca Moresco

A key step towards building single molecule machines is to control the rotation of molecules and nanostructures step by step on a surface. Here, we used the tunneling electrons coming from the tip of a scanning tunneling microscope to achieve the controlled directed rotation of complex o-MeO-DMBI molecules. We studied the adsorption of single o-MeO-DMBI molecules on Au(111) by scanning tunneling microscopy at low temperature. The enantiomeric form of the molecule on the surface can be determined by imaging the molecule by STM at high bias voltage. We observed by lateral manipulation experiments that the molecules chemisorb on the surface and are anchored on Au(111) with an oxygen-gold bond via their methoxy-group. Driven by inelastic tunneling electrons, o-MeO-DMBI molecules can controllably rotate, stepwise and unidirectional, either clockwise or counterclockwise depending on their enantiomeric form.

Entanglement via rotational blockade of MgF molecules in a magic potential

Eunmi Chae

Diatomic polar molecules are one of the most promising platforms of quantum computing due to their rich internal states and large electric dipole moments. Here, we propose entangling rotational states of adjacent polar molecules via a strong electric dipole-dipole interaction. The splitting of 1.27 kHz between two entangled states is predicted for MgF molecules in an optical tweezer array. The resolution of the entangled states can be achieved in a magic potential for the molecules where the rotational states have the same trap frequencies. The magic potential can be formed by tuning the angle between the molecules' quantization axis and the linear polarization of trapping light, so-called magic angle. We calculate the magic angle for MgF molecules in a reasonable experimental condition and obtain that the trap frequencies of the two involved states can be matched within a few 10s of Hz. Establishing entanglement between molecules, our results provide a first step towards quantum computing using diatomic polar molecules.

Physical Chemistry Chemical Physics 23, 1215 (2021)

10.1039/D0CP04042H

MGCVAE: Multi-objective Inverse Design via Molecular Graph Conditional Variational Autoencoder

Myeonghun Lee, Kyoungmin Min

The ultimate goal of various fields is to directly generate molecules with desired properties, such as finding water-soluble molecules in drug development and finding molecules suitable for organic light-emitting diode (OLED) or photosensitizers in the field of development of new organic materials. In this respect, this study proposes a molecular graph generative model based on the autoencoder for de novo design. The performance of molecular graph conditional variational autoencoder (MGCVAE) for generating molecules having specific desired properties is investigated by comparing it to molecular graph variational autoencoder (MGVAE). Furthermore, multi-objective optimization for MGCVAE was applied to satisfy two selected properties simultaneously. In this study, two physical properties -- logP and molar refractivity -- were used as optimization targets for the purpose of designing de novo molecules, especially in drug discovery. As a result, it was confirmed that among generated molecules, 25.89% optimized molecules were generated in MGCVAE compared to 0.66% in MGVAE. Hence, it demonstrates that MGCVAE effectively produced drug-like molecules with two target properties. The results of this study suggest that these graph-based data-driven models are one of the effective methods of designing new molecules that fulfill various physical properties, such as drug discovery.

MolGenSurvey: A Systematic Survey in Machine Learning Models for Molecule Design

Yuanqi Du, Tianfan Fu, Jimeng Sun, Shengchao Liu

Molecule design is a fundamental problem in molecular science and has critical applications in a variety of areas, such as drug discovery, material science, etc. However, due to the large searching space, it is impossible for human experts to enumerate and test all molecules in wet-lab experiments. Recently, with the rapid development of machine learning methods, especially generative methods, molecule design has achieved great progress by leveraging machine learning models to generate candidate molecules. In this paper, we systematically review the most relevant work in machine learning models for molecule design. We start with a brief review of the mainstream molecule featurization and representation methods (including 1D string, 2D graph, and 3D geometry) and general generative methods (deep generative and combinatorial optimization methods). Then we summarize all the existing molecule design problems into several venues according to the problem setup, including input, output types and goals. Finally, we conclude with the open challenges and point out future opportunities of machine learning models for molecule design in real-world applications.

On the possibility of exploring tip-molecule interactions with STM experiments

Christoph Schiel, Philipp Rahe, Philipp Maass

We present a theory for analyzing residence times of single molecules in a fixed detection area of a scanning tunneling microscope (STM). The approach is developed for one-dimensional molecule diffusion and can be extended to two dimensions by using the same methodology. Explicit results are derived for an harmonic attractive and repulsive tip-molecule interaction. Applications of the theory allows one to estimate the type and strength of interactions between the STM tip and the molecule. This includes the possibility of an estimation of molecule-molecule interaction when the tip is decorated by a molecule. Despite our focus on STM, this theory can analogously be applied to other experimental probes that monitor single molecules.

Applying the extended molecule approach to correlated electron transport: important insight from model calculations

Ioan Baldea, Horst Koppel, Robert Maul, Wolfgang Wenzel

Theoretical approaches of electronic transport in correlated molecules usually consider an extended molecule, which includes, in addition to the molecule itself, parts of electrodes. In the case where electron correlations remain confined within the molecule, and the extended molecule is sufficiently large, the current can be expressed by means of Laudauer-type formulae. Electron correlations are embodied into the retarded Green function of a sufficiently large but isolated extended molecule, which represents the key quantity that can be accurately determined by means of ab initio quantum chemical calculations. To exemplify these ideas, we present and analyze numerical results obtained within full CI calculations for an extended molecule described by the interacting resonant level model. Based on them, we argue that for organic electrodes the transport properties can be reliably computed, because the extended molecule can be chosen sufficiently small to be tackled within accurate ab initio methods. For metallic electrodes, larger extended molecules have to be considered in general, but a (semi-)quantitative description of the transport should still be possible particularly in the typical cases where electron transport proceeds by off-resonant tunneling. Our numerical results also demonstrate that, contrary to the usual claim, the ratio between the characteristic Coulomb strength and the level width due to molecule-electrode coupling is not the only quantity needed to assess whether electron correlation effects are strong or weak.

10.1063/1.3455056

Cooperative molecular structure in polaritonic and dark states

Lorenz S. Cederbaum

An ensemble of identical, intrinsically non-interacting molecules exposed to quantum light is discussed. Their interaction with the quantum light induces interactions between the molecules. The resulting hybrid light-matter states exhibit complex structure even if only a single vibrational coordinate per molecule is considered. Since all molecules are identical, it is appealing to start from the uniform situation where all molecules possess the same value of this vibrational coordinate. Then, polaritons and dark states follow like in atoms, but are functions of this coordinate, and this vibrational degree of freedom makes the physics different from that of atoms. However, in spite of all molecules being identical, each molecule does have its own vibrational coordinate. It is thus a vital issue to understand the meaning of the uniform situation and how to depart from it, and enable one to realistically investigate the ensemble. A rigorous and physically relevant meaning of the polariton energy curves in the uniform situation has been found. It is proven that any point on a polariton curve is a minimum or maximum for departing from the uniform situation. It is shown how to explicitly compute the energetic impact of departing from the uniform situation using solely properties of a single free molecule. The dark states and their behavior upon departing from the uniform situation are analyzed as well. Useful techniques not used in this topical domain are introduced and general results on, e.g., minimum energy path, symmetry breaking and restoration, are obtained. It is shown how to transfer the findings to include several or even many nuclear degrees of freedom per molecule and thus to address the problem of quantum light interacting with many complex molecules. The interplay of several degrees of freedom in a single molecule of the ensemble leads to qualitatively different physics.

Measurement of the conductance of a hydrogen molecule

R. H. M. Smit, Y. Noat, C. Untiedt, N. D. Lang, M. van Hemert, J. M. van Ruitenbeek

Recent years have shown steady progress in research towards molecular electronics [1,2], where molecules have been investigated as switches [3-5], diodes [6], and electronic mixers [7]. In much of the previous work a Scanning Tunnelling Microscope was employed to address an individual molecule. As this arrangement does not provide long-term stability, more recently metal-molecule-metal links have been made using break junction devices [8-10]. However, it has been difficult to establish unambiguously that a single molecule forms the contact [11]. Here, we show that a single H2 molecule can form a stable bridge between Pt electrodes. In contrast to results for other organic molecules, the bridge has a nearly perfect conductance of one quantum unit, carried by a single channel. The H2-bridge provides a simple test system and a fundamental step towards understanding transport properties of single-molecule devices.

Nature Vol. 419 (2002) 906-909

10.1038/nature01103

Radius and chirality dependent conformation of polymer molecule at nanotube interface

Chenyu Wei

Temperature dependent conformations of linear polymer molecules adsorbed at carbon nanotube (CNT) interfaces are investigated through molecule dynamics simulations. Model polyethylene (PE) molecules are shown to have selective conformations on CNT surface, controlled by atomic structures of CNT lattice and geometric coiling energy. PE molecules form entropy driven assembly domains, and their preferred wrapping angles around large radius CNT (40, 40) reflect the molecule configurations with energy minimums on a graphite plane. While PE molecules prefer wrapping on small radius armchair CNT (5, 5) predominantly at low temperatures, their configurations are shifted to larger wrapping angle ones on a similar radius zigzag CNT (10, 0). A nematic transformation around 280 K is identified through Landau-deGennes theory, with molecule aligning along tube axis in extended conformations

10.1021/nl0605770

A Mott-like State of Molecules

S. Dürr, T. Volz, N. Syassen, D. M. Bauer, E. Hansis, G. Rempe

We prepare a quantum state where each site of an optical lattice is occupied by exactly one molecule. This is the same quantum state as in a Mott insulator of molecules in the limit of negligible tunneling. Unlike previous Mott insulators, our system consists of molecules which can collide inelastically. In the absence of the optical lattice these collisions would lead to fast loss of the molecules from the sample. To prepare the state, we start from a Mott insulator of atomic 87Rb with a central region, where each lattice site is occupied by exactly two atoms. We then associate molecules using a Feshbach resonance. Remaining atoms can be removed using blast light. Our method does not rely on the molecule-molecule interaction properties and is therefore applicable to many systems.

10.1063/1.2400658

Time invariance violation in photon-atom and photon-molecule interactions

V. A. Kuz'menko

A direct experimental proof of very strong T-invariance violation in interactions of the photons with atoms and molecules exists in the molecular physics.

Discreteness-Induced Transitions in Autocatalytic Systems

Yuichi Togashi, Kunihiko Kaneko

To study the dynamics of chemical processes, we often adopt rate equations to observe the change in chemical concentrations. However, when the number of the molecules is small, the fluctuations cannot be neglected. We often study the effects of fluctuations with the help of stochastic differential equations. Chemicals are composed of molecules on a microscopic level. In principle, the number of molecules must be an integer, which must only change discretely. However, in analysis using stochastic differential equations, the fluctuations are regarded as continuous changes. This approximation can only be valid if applied to fluctuations that involve a sufficiently large number of molecules. In the case of extremely rare chemical species, the actual discreteness of the molecules may critically affect the dynamics of the system. To elucidate the effects of the discreteness, we study an autocatalytic system consisting of several interacting chemical species with a small number of molecules through stochastic particle simulations. We found novel states, which were characterized as an extinction of molecule species, due to the discrete nature of the molecules. We also observed a strong dependence of the chemical concentrations on the size of the system, which was caused by transitions to the novel states.

Dwell time of a Brownian interacting molecule in a cellular microdomain

Adi Taflia, David Holcman

The time spent by an interacting Brownian molecule inside a bounded microdomain has many applications in cellular biology, because the number of bounds is a quantitative signal, which can initiate a cascade of chemical reactions and thus has physiological consequences. In the present article, we propose to estimate the mean time spent by a Brownian molecule inside a microdomain $\Omega$ which contains small holes on the boundary and agonist molecules located inside. We found that the mean time depends on several parameters such as the backward binding rate (with the agonist molecules), the mean escape time from the microdomain and the mean time a molecule reaches the binding sites (forward binding rate). In addition, we estimate the mean and the variance of the number of bounds made by a molecule before it exits $\Omega$. These estimates rely on a boundary layer analysis of a conditional mean first passage time, solution of a singular partial differential equation. In particular, we apply the present results to obtain an estimate of the mean time spent (Dwell time) by a Brownian receptor inside a synaptic domain, when it moves freely by lateral diffusion on the surface of a neuron and interacts locally with scaffolding molecules.

Controlling Polar Molecules in Optical Lattices

S. Kotochigova, E. Tiesinga

We investigate theoretically the interaction of polar molecules with optical lattices and microwave fields. We demonstrate the existence of frequency windows in the optical domain where the complex internal structure of the molecule does not influence the trapping potential of the lattice. In such frequency windows the Franck-Condon factors are so small that near-resonant interaction of vibrational levels of the molecule with the lattice fields have a negligible contribution to the polarizability and light-induced decoherences are kept to a minimum. In addition, we show that microwave fields can induce a tunable dipole-dipole interaction between ground-state rotationally symmetric (J=0) molecules. A combination of a carefully chosen lattice frequency and microwave-controlled interaction between molecules will enable trapping of polar molecules in a lattice and possibly realize molecular quantum logic gates. Our results are based on ab initio relativistic electronic structure calculations of the polar KRb and RbCs molecules combined with calculations of their rovibrational motion.

10.1103/PhysRevA.73.041405

Photonic molecules made of matched and mismatched microcavities: new functionalities of microlasers and optoelectronic components

Svetlana V. Boriskina, Trevor M. Benson, Phillip Sewell

Photonic molecules, named by analogy with chemical molecules, are clusters of closely located electromagnetically interacting microcavities or "photonic atoms". As two or several microcavities are brought close together, their optical modes interact, and a rich spectrum of photonic molecule supermodes emerges, which depends both on geometrical and material properties of individual cavities and on their mutual interactions. Here, we discuss ways of controllable manipulation of photonic molecule supermodes, which improve or add new functionalities to microcavity-based optical components. We present several optimally-tuned photonic molecule designs for lowering thresholds of semiconductor microlasers, producing directional light emission, enhancing sensitivity of microcavity-based bio(chemical)sensors, and optimizing electromagnetic energy transfer around bends of coupled-cavity waveguides. Photonic molecules composed of identical microcavities as well as of microcavities with various degrees of size or material detuning are discussed. Microwave experiments on scaled photonic molecule structures are currently under way to confirm our theoretical predictions.

Proc. SPIE, vol. 6452, 6452X, Feb. 2007

10.1117/12.714344

Molecular coupling of light with plasmonic waveguides

Anton Kuzyk, Mika Pettersson, J. Jussi Toppari, Tommi K. Hakala, Hanna Tikkanen, Henrik Kunttu, Paivi Torma

We use molecules to couple light into and out of microscale plasmonic waveguides. Energy transfer, mediated by surface plasmons, from donor molecules to acceptor molecules over ten micrometer distances is demonstrated. Also surface plasmon coupled emission from the donor molecules is observed at similar distances away from the excitation spot. The lithographic fabrication method we use for positioning the dye molecules allows scaling to nanometer dimensions. The use of molecules as couplers between far-field and near-field light offers the advantages that no special excitation geometry is needed, any light source can be used to excite plasmons and the excitation can be localized below the diffraction limit. Moreover, the use of molecules has the potential for integration with molecular electronics and for the use of molecular self-assembly in fabrication. Our results constitute a proof-of-principle demonstration of a plasmonic waveguide where signal in- and outcoupling is done by molecules.

Optics Express, Vol. 15, Issue 16, pp. 9908-9917, 2007

10.1364/OE.15.009908

A first principles study on organic molecules encapsulated BN nanotubes

Wei He, Zhenyu Li, Jinlong Yang, J. G. Hou

The electronic structures of boron nitride nanotubes (BNNTs) doped by organic molecules are investigated with density functional theory. Electrophilic molecule introduces acceptor states in the wide gap of BNNT close to the valence band edge, which makes the doped system a $p$-type semiconductor. However, with typical nucleophilic organic molecules encapsulation, only deep occupied molecular states but no shallow donor states are observed. There is a significant electron transfer from BNNT to electrophilic molecule, while the charge transfer between nucleophilic molecule and BNNT is neglectable. When both electrophilic and nucleophilic molecules are encapsulated in the same BNNT, large charge transfer between the two kinds of molecules occurs. The resulted small energy gap can strongly modify the transport and optical properties of the system.

Journal of Chemical Physics 128, 164701-5 (2008)

10.1063/1.2901026