Ground State Of Molecule Research Articles

Exploring Transient States of PAmKate to Enable Improved Cryogenic Single-Molecule Imaging.

Super-resolved cryogenic correlative light and electron microscopy is a powerful approach which combines the single-molecule specificity and sensitivity of fluorescence imaging with the nanoscale resolution of cryogenic electron tomography. Key to this method is active control over the emissive state of fluorescent labels to ensure sufficient sparsity to localize individual emitters. Recent work has identified fluorescent proteins (FPs) that photoactivate or photoswitch efficiently at cryogenic temperatures, but long on-times due to reduced quantum yield of photobleaching remain a challenge for imaging structures with a high density of localizations. In this work, we explore the photophysical properties of the red photoactivatable FP PAmKate and identify a 2-color process leading to enhanced turn-off of active emitters, improving localization rate. Specifically, after excitation of ground state molecules, we find that a transient state forms with a lifetime of ∼2 ms under cryogenic conditions, which can be bleached by exposure to a second wavelength. We measure the response of the transient state to different wavelengths, demonstrate how this mechanism can be used to improve imaging, and provide a blueprint for the study of other FPs at cryogenic temperatures.

Magnetically Tunable Electric Dipolar Interactions of Ultracold Polar Molecules in the Quantum Ergodic Regime.

By leveraging the hyperfine interaction between the rotational and nuclear spin degrees of freedom, we demonstrate extensive magnetic control over the electric dipole moments, electric dipolar interactions, and ac Stark shifts of ground-state alkali-dimer molecules such as KRb(X^{1}Σ^{+}). The control is enabled by narrow avoided crossings and the highly ergodic character of molecular eigenstates at low magnetic fields, offering a general and robust way of continuously tuning the intermolecular electric dipolar interaction for applications in quantum simulation, quantum sensing, and dipolar spinor physics.

Atomic momentum distributions in polyatomic molecules in rotational-vibrational eigenstates.

We report a quantum mechanical method for calculating the momentum distributions of constituent atoms of polyatomic molecules in rotational-vibrational eigenstates. Application of the present theory to triatomic molecules in the rovibrational ground state revealed that oscillatory changes appear on the proton momentum distribution in the nonlinear H2O molecule, while no such modulation is present in the case of an oxygen atom in the linear CO2 molecule. The atomic momentum distributions were analyzed in detail by means of a rigid rotor model, and it was found that the oscillation originates from the quantum-mechanical delocalization of the target atom with respect to the other atoms.

Exploring transient states of PAmKate to enable improved cryogenic single-molecule imaging.

Super-resolved cryogenic correlative light and electron microscopy is a powerful approach which combines the single-molecule specificity and sensitivity of fluorescence imaging with the nanoscale resolution of cryogenic electron tomography. Key to this method is active control over the emissive state of fluorescent labels to ensure sufficient sparsity to localize individual emitters. Recent work has identified fluorescent proteins (FPs) which photoactivate or photoswitch efficiently at cryogenic temperatures, but long on-times due to reduced quantum yield of photobleaching remains a challenge for imaging structures with a high density of localizations. In this work, we explore the photophysical properties of the red photoactivatable FP PAmKate and identify a 2-color process leading to enhanced turn-off of active emitters, improving localization rate. Specifically, after excitation of ground state molecules, we find a transient state forms with a lifetime of ~2 ms under cryogenic conditions which can be bleached by exposure to a second wavelength. We measure the response of the transient state to different wavelengths, demonstrate how this mechanism can be used to improve imaging, and provide a blueprint for study of other FPs at cryogenic temperatures.

Chemical simulations of quantum systems using quantum computers - review of algorithms and their experimental verification

Computer simulations using ever-increasing computing power and machine learning techniques allow advanced molecular modelling, molecular dynamics simulations and studies of intermolecular interactions. However, due to the complexity of biological systems and chemical processes at the molecular level, their accurate representation using classical computer models and techniques has faced a number of significant limitations for many years. A new and promising direction for the development of computational science and its potential applications in biochemistry is quantum computing and its integration with classical high-performance supercomputing systems. This article responds to the growing interest in the use of available quantum computers in exemplary applications. In this paper, we aim to provide an overview of the basic notions involved in the development of quantum algorithms and simulations related to issues at the interface of quantum chemistry and biochemistry. In addition, the article introduces the basic principles of performing simulations using the state-of-the-art quantum computers in the era of Noisy Intermediate-Scale Quantum (NISQ). Experimental results of the classical-quantum algorithm Variational Quantum Eigensolver (VQE) for example molecules H2 and CH+ are also presented. Despite the many shortcomings of currently available quantum computers, the analysed VQE algorithm proved to be effective in approximating the ground state of molecules using a minimal functional basis.

Utilizing the Hartree-Fock Method to Analyze Carbon Dioxide Molecule

The determination of the ground state of the carbon dioxide molecule is conducted through matrix Hartree-Fock computations for a polyatomic molecule. Utilization of basis sets is implemented to achieve a precision that approaches the sub-μ Hartree of the CO<sub>2</sub> molecule for the energy levels. Utilizing a 28s14p14d14f atom-centered and a 24sl0plld bond-centered Gaussian basis set, the upper limit for the Hartree-Fock ground state energy of CO<sub>2</sub> at its practical picture has been calculated, yielding a value of -187.125408 Hartree. Utilizing our knowledge in diatomic molecules, we approximate the precision of this measurement to fall within 5-6 μ Hartree. The current computations offer a methodology to assess the precision of different basis sets frequently utilized in molecular self-consistent field investigations. These basis sets encompass STOJG, 4-31G, 6-31G, 6-31G(3d), 6-31IG, 6-311+G(3d0, D95, and D95V+(3d)), alongside cc-pVDZ, uug-cc-pVDZ, cc-pVTZ, and aug-cc-pVTZ, which have been proposed for the purpose of investigating electron correlation. We have recently performed calculations on the CO1 ground state at the nuclear geomevy employed in the presenl work using the basis sets proposed by Dunning and co-workers and designated cc-pVQZ. aupcc-pVQZ, cc-pVSZ and nupcc-pVSZ. The estimated basis set truncation emrs for these sets are 0.00371, 0.003 19, 0.00047 and 0.00039 Hartree respectively.

Simulation of the Stark/Zeeman-hyperfine-rotational spectra of 79BrF molecule within its vibronic ground state

Transition dipole moments of Stark/Zeeman-hyperfine-rotational spectra of [Formula: see text] within the vibronic ground state of BrF molecule are deduced, and thus, the transition selection rules are summarized. Unlike the nearly equal linewidth in the other spectral region, the hyperfine-rotational spectral linewidth strongly depends on its transition probability due to the only natural broadening acts. Thereafter, the Stark/Zeeman-hyperfine-rotational spectra are simulated, which could help to assign the experimental spectra. In addition, the quadratic dependence of the Stark spectral shift on the applied electric field is fitted with the fitting correlation of 0.9999, which may be applied in the mapping of a complex electrostatic field. Our results are helpful for the investigations of the field-controlled cold molecular collision, the cold molecular manipulation, the cold molecular further cooling, and other related aspects as well.

Excited-State Dynamics of Carbazole and tert-Butyl-Carbazole in Thin Films

Thin films of carbazole (Cz) derivatives are frequently used in organic electronics, such as organic light-emitting diodes (OLEDs). Because of the proximity of the Cz units, the excited-state relaxation in such films is complicated, as intermolecular pathways, such as singlet–singlet annihilation (SSA), kinetically compete with the emission. Here, we provide an investigation of two benchmark systems employing neat carbazole and 3,6-di-tert-butylcarbazole (t-Bu-Cz) films and also their thin film blends with poly(methyl methacrylate) (PMMA). These are investigated by a combination of atomic force microscopy (AFM), femtosecond and nanosecond transient absorption spectroscopy (fs-TA and ns-TA) and time-resolved fluorescence. Excitonic J-aggregate-type features are observed in the steady-state absorption and emission spectra of the neat films. The S1 state shows a broad excited-state absorption (ESA) spanning the entire UV–Vis–NIR range. At high S1 exciton number densities of about 4 × 1018 cm−3, bimolecular diffusive S1–S1 annihilation is found to be the dominant SSA process in the neat films with a rate constant in the range of 1–2 × 10−8 cm3 s−1. SSA produces highly vibrationally excited molecules in the electronic ground state (S0*), which cool down slowly by heat transfer to the quartz substrate. The results provide relevant photophysical insight for a better microscopic understanding of carbazole relaxation in thin-film environments.

Optimal preparation of Bose and Fermi atomic gas mixtures of 87Rb and 40K in a crossed optical dipole trap

We report on the optimal production of the Bose and Fermi mixtures with 87Rb and 40K in a crossed optical dipole trap (ODT). We measure the atomic number and lifetime of the mixtures in combination of the spin state |F = 9/2, m F = 9/2〉 of 40K and |1, 1〉 of 87Rb in the ODT, which is larger and longer compared with the combination of the spin state |9/2, 9/2〉 of 40K and |2, 2〉 of 87Rb in the ODT. We observe the atomic numbers of 87Rb and 40K shown in each stage of the sympathetic cooling process while gradually reducing the depth of the optical trap. By optimizing the relative loading time of atomic mixtures in the MOT, we obtain the large atomic number of 40K (∼6 × 106) or the mixtures of atoms with an equal number (∼1.6 × 106) at the end of evaporative cooling in the ODT. We experimentally investigate the evaporative cooling in an enlarged volume of the ODT via adding a third laser beam to the crossed ODT and found that more atoms (8 × 106) and higher degeneracy (T/T F = 0.25) of Fermi gases are obtained. The ultracold atomic gas mixtures pave the way to explore phenomena such as few-body collisions and the Bose–Fermi Hubbard model, as well as for creating ground-state molecules of 87Rb40K.

Aromaticity in the Electronic Ground and Lowest Triplet States of Molecules with Fused Thiophene Rings.

Analysis of the variations of the off-nucleus isotropic magnetic shielding, σiso(r), around thiophene, thienothiophenes, dithienothiophenes and sulflowers in their electronic ground (S0) and lowest triplet (T1) states reveals that some of the features of aromaticity and bonding in these molecules do not fit in with predictions based on the popular Hückel's and Baird's rules. Despite having 4n π electrons, the S0 states of the sulflowers are shown to be aromatic, due to the local aromaticities of the individual thiophene rings. To reduce its T1 antiaromaticity, the geometry of thiophene changes considerably between S0 and T1: In addition to losing planarity, the carbon-carbon two 'double' and one 'single' bonds in S0 turn into two 'single' and one 'double' bonds in T1. Well-defined Baird-style aromaticity reversals are observed between the S0 and T1 states of only three of the twelve thiophene-based compounds investigated in this work, in contrast, the sulflower with six thiophene rings which is weakly aromatic in S0 becomes more aromatic in T1. The results suggest that the change in aromaticity between the S0 and T1 states in longer chains of fused rings is likely to affect mostly the central ring (or the pair of central rings); rings sufficiently far away from the central ring(s) can retain aromatic character.

Probing the in-plane dipole moment vector between ground and excited state of single molecules by the Stark effect.

Single molecules, embedded inside a well-defined insertion site of a single-crystalline host matrix, are sensitive probes of electric field via the induced Stark shift on their lifetime-limited electronic transition. Though the response of molecules to electric field has been shown to be relatively homogeneous, crystal symmetry allows for several, spectroscopically-indistinguishable, orientations of the net permanent dipole moment between the ground and excited state - the dipole vector - and this is problematic for measuring field orientation and magnitude. In this work, we measure for each terrylene molecule, embedded inside a new host matrix, the dipole vector independently by an electric field that we can rotate in the plane of the crystal. This single crystal host matrix, called [1]BenzoThieno[3,2-b]BenzoThiophene, induces a moderate symmetry breaking of the embedded centrosymmetric terrylene molecule, and gives rise to a net dipole moment of 0.28±0.09 Debye. Based on quantum chemistry calculations we propose an insertion site that best matches the experimental findings.

Coherent anti-Stokes Raman scattering spectral calculation and vibrational-rotational temperature measurement of non-equilibrium plasma flow field

How to characterize thermodynamic non-equilibrium characteristics of flow field accurately and reliably is the key to solving the thermal and chemical non-equilibrium problem, which is one of the most basic scientific problems in hypersonic aerodynamcis. Based on the principles of coherent anti-Stokes Raman scattering (CARS) and modified exponential gap (MEG) Raman linewidth model, a CARS spectral computation and vib-rotational temperature inversion program is proposed for characterizing the thermodynamic non-equilibrium properties of high-temperature gas flow field. The influence of vibrational temperature and rotational temperature on Raman linewidth and CARS spectral characteristics are studied theoretically. A CARS system is built and the corresponding accuracy in a wide temperature range is verified in a static environment that is established by using a high-temperature tube furnace and a McKenna burner. The results show that the average relative deviation of the vibration temperature <i>T</i><sub>v</sub> and rotational temperature <i>T</i><sub>r</sub> from the equilibrium temperature <i>T</i><sub>eq</sub> are 4.28% and 3.34% respectively in a range of 1000 to 2300 K, and the corresponding average repeatability is 1.95% and 3.03% respectively. These results indicate that the vibrational temperature and rotational temperature obtained by the non-equilibrium program are in good agreement with those obtained from the thermal equilibrium program. Finally, a non-equilibrium microwave plasma flow is built and its vibrational temperature and rotational temperature are obtained by using the developed program. The results show that the microwave plasma is in thermodynamic non-equilibrium, and the vibrational temperature and rotational temperature are proportional to microwave power, while the thermodynamic non-equilibrium degree exhibits an opposite trend. With microwave power increasing from 80 to 180 W, the vibrational temperature of plasma increases from (2201 ± 43) K to (2452 ± 56) K, the rotational temperature increases from (382 ± 20) K to (535 ± 49) K, for which the principal reasons are that the increase in microwave power leads to an increase in electron number density, and neutral particles obtain energy through collision with electrons, resulting in the increase of vibrational temperature, rotational temperature, and translational temperature. The thermodynamic non-equilibrium degree decreases from 0.83 to 0.78 with the microwave power increasing, which is due to the V-T relaxation rate increasing. The molecules in the excited vibrational states lose energy through collision with ground state molecules (i.e. V-T relaxation process), leading the vibrational energy to be converted into translational energy. For N<sub>2</sub> molecules, the V-T relaxation rate is directly proportional to the temperature, which causes the difference between vibrational temperature and rotational temperature to decrease with microwave power increasing, and non-equilibrium degree to decrease with microwave power increasing as well.

Unlocking flavin photoacid catalysis through electrophotochemistry.

Molecular flavins are one of the most versatile photocatalysts. They can coordinate single and multiple electron transfer processes, gift hydrogen atoms, form reversible covalent linkages that support group transfer mechanisms, and impart photonic energy to ground state molecules, priming them for downstream reactions. But one mechanism that has not featured extensively is the ability of flavins to act as photoacids. Herein, we disclose our proof-of-concept studies showing that electrophotochemistry can transform fully oxidized flavin quinones to super-oxidized flavinium photoacids that successfully guide proton-transfer and deliver acid-catalyzed products. We also show that these species can adopt a second mechanism wherein they react with water to release hydroxyl radicals that facilitate hydrogen-atom abstraction and sp3C-H functionalization protocols. Together, this unprecedented bimodal reactivity enables electro-generated flavinium salts to affect synthetic chemistries previously unknown to flavins, greatly expanding their versatility as catalysts.

An examination of the effectiveness of the expired drug isoprinosine in preventing aluminum corrosion in alkaline solutions using both computational and experimental techniques.

A now-expired medication called isoprinosine was examined in NaOH (0.50 M) solutions as a potential novel inhibitor of aluminum corrosion. The inhibitory effectiveness of the isoprinosine compounds was examined utilizing different electrochemical tests (open circuit potential OCP, potentiodynamic polarization and electrochemical impedance spectroscopy EIS), surface examination and quantum calculations. Increases in isoprinosine concentration were seen to increase the inhibitory efficacy. It was discovered that the inhibitory action, which results in the inhibition of charge and mass transfer and protects the aluminum against harmful ions, was brought on by isoprinosine molecules adhering to the aluminum surface. Additionally, the surface morphology of Al dissolved in a 0.50 M NaOH solution without and with the existence of an isoprinosine molecule was analyzed using SEM/EDX and AFM techniques. Utilizing the optimized geometric parameters of the ground state molecules, FMO simulations and additional studies were executed successfully utilizing the density functional theory (DFT/B3LYP/6-311++G(d,p)). Based on the expected energies for the molecular carriers of charge, HOMO and LUMO. Calculations are also done for the AIM charges, Fukui functions, AIM charges, and excitation energies. Furthermore, molecular dynamic was simulated to explore the corrosion inhibition efficiency and mechanism of inhibition. The computational results are in the same agreement with experimental results, showing that isoprinosine can inhibit the corrosion of aluminum in 0.5 M NaOH.

An association sequence suitable for producing ground-state RbCs molecules in optical lattices

We identify a route for the production of ^{87}87Rb^{133}133Cs molecules in the X^1\Sigma^+X1Σ+ rovibronic ground state that is compatible with efficient mixing of the atoms in optical lattices. We first construct a model for the excited-state structure using constants found by fitting to spectroscopy of the relevant a\,^3 \Sigma^+ → b\, ^3\Pi_1a3Σ+→b3Π1 transitions at 181.5 G and 217.1 G. We then compare the predicted transition dipole moments from this model to those found for the transitions that have been successfully used for STIRAP at 181.5 G. We form molecules by magnetoassociation on a broad interspecies Feshbach resonance at 352.7 G and explore the pattern of Feshbach states near 305 G. This allows us to navigate to a suitable initial state for STIRAP by jumping across an avoided crossing with radiofrequency radiation. We identify suitable transitions for STIRAP at 305 G. We characterize these transitions experimentally and demonstrate STIRAP to a single hyperfine level of the ground state with a one-way efficiency of 85(4)%.

Spectroscopic properties (FT-IR, NMR and UV) and DFT studies of amodiaquine

Amodiaquine (AQ) was synthesized by a condensation reaction and characterized by experimental FT-IR, 1H and 13C nuclear magnetic resonance (NMR) and UV spectroscopies. In the present work, Density Functional Theory (DFT) calculations using B3LYP method with 6–311++G(d,p) and 6–311++G(2d, p) basis sets were performed, first, to confirm its structure, then to explain its reactive nature through its molecular properties such as natural charges, local and global reactivity descriptors or natural bond orbital (NBO). The 1H and 13C NMR chemical shifts were calculated by using the gauge-independent atomic orbital (GIAO) method, while the electronic UV–Vis spectrum is predicted using the time-dependent density functional theory (TD-DFT). Globally, the computerized results showed close similarity with the experimental values.The calculated energy band gap (ELUMO-EHOMO) value of AQ was found to be 4.09 eV suggesting that it could be considered as a hard molecule with high stability, supported by global reactivity descriptors. Molecular electrostatic potential (MEP) analysis revealed heteroatoms (oxygen and nitrogen) as the most putative nucleophilic sites when hydrogen atoms to which they are linked appear as electrophilic sites. The potential use of amodiaquine as non-linear optical (NLO) material and its thermodynamic indicators have also been assessed.

A new route to associating ultracold polar molecules in the absolute ground state

A new route to associating ultracold polar molecules in the absolute ground state

Excited state dynamics of bay and peri benzothienyl perylene to understand the excimer formation and its dissociation

Many planar acenes such as pyrene, perylene etc. are known to form dimeric complex of their ground and excited state (excimer formation). Relaxation of excimer, carrier mobility & exciton diffusion in the solid state, and even singlet fission depends on the interaction between ground and excited state molecules in excimer. The role of excimer in triplet formation can be understood by: S0↑↓+S1↑↓⇄{S1S01↑↓↑↓}⇄{T1T11↑↑↓↓}⇄T1↑↑+T1↓↓. Intermediate excimer (T1T1)1 formation i.e., (SnS0)1 → (T1T1)1, and its decay to triplets have been studied by several groups, however, reports on the dissociation of excimer are very few. In this work, we aimed to study the dynamics of excimer formation and its further dissociation using perylene derivatives. We synthesized two positional isomers of benzothienyl substituted perylene i.e., peri-BT and bay-BT, and studied their photophysical properties in solution, nanoaggregates, and thermally evaporated thin films. Excited state dynamics in thin films suggest the dissociation of 1(excimer) to a monomeric singlet excited state in a microsecond timescale. Transient absorption spectral characteristics suggest the formation of a charge transfer state within picoseconds, followed by decay to a long-lived (few microseconds) excimer state. The formation of CT is promoted by strong intermolecular interaction in the thin film.

Collisionally stable gas of bosonic dipolar ground-state molecules

Collisionally stable gas of bosonic dipolar ground-state molecules

Plasma-parameter dependence of ro-vibrational temperatures for H2 in LHD divertor

We analyzed a thousand visible spectra of Fulcher-α band measured for divertor plasmas in Large Helical Device. With a coronal model and Bayesian inference, the population distribution of hydrogen molecule in the electronic ground state was estimated. The non-thermal population distribution was recovered with a two-temperature model, which has two sets of rotational and vibrational temperatures, as well as their mixture coefficient. The lower rotational temperature significantly changes according to the plasma parameters. Its nearly linear dependence on the electron density was found, which is consistent with previous works. The lower vibrational temperature also shows a small density dependence, as reported by a previous work. On the other hand, the higher rotational and vibrational temperatures as well as the mixture coefficient only show slight changes over the broad range of plasma parameters. These population parameters show a significant correlation; with higher electron density, all the temperatures and the fraction of the higher-temperature component increase simultaneously. This suggests that the electron impact plays an important role to determine the population distribution.