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Rapid advancements in nanotechnology have allowed for the characterization of single molecules by placing them in the vicinity of nanoplasmonic structures that are known to confine light to sub-molecular scales. In this study, we introduce a theoretical framework that captures higher-order effects, and we explore the limits of the standard description of a molecular emitter as a point-dipole. We particularly focus on the role played by the emitter chain length and electron conjugation. Strong deviations are observed from the point-dipole approximation, demonstrating that higher-order effects are essential to fully capture the emission rate of extended molecules in the vicinity of nanoparticles. This deviation strongly depends on the orientation of the conjugated chain relative to the nanoplasmonic structure. Finally, we propose a simple rationalization that qualitatively assesses the difference from the point-dipole approximation. [ABSTRACT FROM AUTHOR]

Absolute line strength measurements of hydroperoxyl (HO2) radical in the OO-stretching (ν3) fundamental band have been performed by means of mid-infrared time-resolved dual-comb spectroscopy. By employing two sets of dual-comb spectrometers, high-resolution time-resolved spectra of HO2 and HCl, formed in the photolysis reaction system of Cl2/CH3OH/O2, could be, respectively, measured near 1123 and 3059 cm−1. With kinetic simulations, spectral analysis of both HO2 and HCl, as well as the accurate line strength of the HCl R(9) transition at 3059.316 cm−1, an absolute line strength of the ν3 131,13 ← 121,12 F1,2 transitions in HO2 at 1122.983 cm−1 was first determined to be 1.80 × 10−20 cm molecule−1 with a small uncertainty down to 4% under the conditions with low initial concentrations of Cl radical (1.63–1.81 × 1013 molecule cm−3). Furthermore, broadband high-resolution spectra of the ν3 fundamental band of HO2 were recorded in the range of 1088–1124 cm−1 with an average spectral resolution of 0.002 cm−1. By contour fitting the measured broadband spectra with PGOPHER, the line strengths of hundreds of rovibrational transitions were obtained relative to the well-determined HO2 lines at 1122.983 cm−1, and those values were observed to be higher than those tabulated in the HITRAN database by a factor of ∼2.8. Moreover, the absolute band strength of the ν3 fundamental band in HO2 was derived to be 22.3 km mol−1 with an uncertainty of 5%. This work providing precise and detailed spectral data would be crucial in revisiting the theoretical modeling of HO2 geometry and updating the database of the HO2 radical. [ABSTRACT FROM AUTHOR]

Single-Molecule Junctions (SMJs) are key platforms for the exploration of electron transport at the molecular scale. In this study, we present a method that employs different exchange-correlation density functionals for the molecule and the lead domains in an SMJ, enabling the selection of the optimal one for each part. This is accomplished using a formally exact projection-based density-functional theory (DFT-in-DFT) embedding technique combined with the non-equilibrium Green's function method to predict zero-bias conductance. The effectiveness of this approach is illustrated through transport calculations on SMJs with benzene-1,4-diamine and its tetramethylated and tetrafluorinated variants, using the CAM-B3LYP range-separated hybrid functional for the embedded molecule and the Perdew–Burke–Ernzerhof (PBE) functional for the electrodes. The findings indicate a substantial improvement in the accuracy of the predicted zero-bias conductance compared to traditional modeling using the PBE functional across the entire system. The causes for the noted improvement are demonstrated through the examination of alterations in the energy levels of the embedded molecule, along with variations in the electrode–molecule interactions. [ABSTRACT FROM AUTHOR]

How condensed-matter simulations depend on the number of molecules being simulated (N) is sometimes itself a valuable piece of information. Liquid crystals provide a case in point. Light scattering and 2d-IR experiments on isotropic-phase samples display increasingly large orientational fluctuations ("pseudo-nematic domains") as the samples approach their nematic phase. The growing length scale of those locally ordered domains is readily seen in simulation as an ever-slower convergence of the distribution of orientational order parameters with N. But the rare-event character and exceptionally slow time scales of the largest fluctuations make them difficult to sample accurately. We show in this paper how taking a large-deviation-theory perspective enables us to leverage simulation-derived information more effectively. A key insight of the theory is that finding quantities such as orientational order parameters (extensive variables) is completely equivalent to deducing the conjugate (intensive) thermodynamic field required to equilibrate that amount of order—and that knowing the relationship between the two (the "equation of state") can easily be turned into knowing the relative free energy of that degree of order. A variety of well-known thermodynamic integration strategies are already founded on this idea, but instead of applying an artificially imposed external field, we use a priori statistical mechanical insights into the small and large-field limits to construct a simulation-guided, interpolated, equation of state. The free energies that result mostly need information from the most probable configurations, making the simulation process far more efficient than waiting for (or artificially generating) large fluctuations. [ABSTRACT FROM AUTHOR]

Rigid, non-polarizable water models are very efficient from a computational point of view, and some of them have a great ability in predicting experimental properties. There is, however, little room for improvement in simulating water with this strategy, whose main shortcoming is that water molecules do not change their interaction parameters in response to the local molecular landscape. In this work, we propose a novel modeling strategy that involves using two rigid non-polarizable models as states that water molecules can adopt depending on their molecular environment. During the simulation, molecules dynamically transition from one state to another depending on a local order parameter that quantifies some local structural feature. In particular, molecules belonging to low- and high-tetrahedral order environments are represented with the TIP4P/2005 and TIP4P/Ice rigid models, respectively. In this way, the interaction between water molecules is strengthened when they acquire a tetrahedral coordination, which can be viewed as an effective way of introducing polarization effects. We call the resulting model TIP 4 P 2005 Ice and show that it outperforms either of the rigid models that build it. This multi-state strategy only slows down simulations by a factor of 1.5 compared to using a standard non-polarizable model and holds great promise for improving simulations of water and aqueous solutions. [ABSTRACT FROM AUTHOR]

Active learning (AL) has shown promise to be a particularly data-efficient machine learning approach. Yet, its performance depends on the application, and it is not clear when AL practitioners can expect computational savings. Here, we carry out a systematic AL performance assessment for three diverse molecular datasets and two common scientific tasks: compiling compact, informative datasets and targeted molecular searches. We implemented AL with Gaussian processes (GP) and used the many-body tensor as molecular representation. For the first task, we tested different data acquisition strategies, batch sizes, and GP noise settings. AL was insensitive to the acquisition batch size, and we observed the best AL performance for the acquisition strategy that combines uncertainty reduction with clustering to promote diversity. However, for optimal GP noise settings, AL did not outperform the randomized selection of data points. Conversely, for targeted searches, AL outperformed random sampling and achieved data savings of up to 64%. Our analysis provides insight into this task-specific performance difference in terms of target distributions and data collection strategies. We established that the performance of AL depends on the relative distribution of the target molecules in comparison to the total dataset distribution, with the largest computational savings achieved when their overlap is minimal. [ABSTRACT FROM AUTHOR]

As the temperature decreases, rigid anisotropic molecules that usually incorporate polar groups, aromatic rings or multiple bonds, orient along a common direction, eventually forming liquid-crystalline phases under specific thermodynamic conditions. This study explores the phase behavior and dynamics of board-shaped mesogens with a 1,4,5,8-tetraphenyl-anthraquinone core and four lateral arms forming an oligo(phenyleneethynylene) scaffold. These molecules are promising candidates for forming the elusive biaxial nematic phase. Through atomistic molecular dynamics simulations, we observe the formation of nematic and smectic liquid crystals, in qualitative agreement with experimental observations. To characterize the structure, we compute pair correlation functions along relevant symmetry directions and the nematic order parameter, which indicate a dominant uniaxial ordering with very weak biaxiality. In addition, we analyze the dynamics of our board-shaped mesogens along and perpendicular to the nematic director, revealing an intriguing non-Gaussian behavior and dynamical heterogeneities, with coexisting slow and fast molecules. Building on our recent simulations at the colloidal scale, which demonstrated that monodisperse board-like particles are unable to form biaxial nematics while polydisperse particles can, we hypothesize that a similar behavior may occur at the molecular scale in mixtures of molecules. Although pure-component molecular systems reveal weak biaxiality, our findings suggest that investigating mixtures of the most promising candidates, those molecules that form nematic or smectic phases, could uncover conditions conducive to the formation of biaxial nematic liquid crystals. [ABSTRACT FROM AUTHOR]

Based on our previous study [Wang et al., J. Chem. Phys. 153, 184102 (2020)], we generalize the theory of molecular emission power spectra (EPS) from one molecule to multichromophoric systems in the framework of macroscopic quantum electrodynamics. This generalized theory is applicable to ensembles of molecules, providing a comprehensive description of the molecular spontaneous emission spectrum in arbitrary inhomogeneous, dispersive, and absorbing media. In the far-field region, the analytical formula of EPS can be expressed as the product of a lineshape function (LF) and an electromagnetic environment factor (EEF). To demonstrate the polaritonic effect on multichromophoric systems, we simulate the LF and EEF for one to three molecules weakly coupled to surface plasmon polaritons above a silver surface. Our analytical expressions show that the peak broadening originates from not only the spontaneous emission rates but also the imaginary part of resonant dipole–dipole interactions (non-Hermitian interactions), which is associated with the superradiance of molecular aggregates, indicating that the superradiance rate can be controlled through an intermolecular distance and the design of dielectric environments. This study presents an alternative approach to directly analyze the hybrid-state dynamics of multichromophoric systems coupled with polaritons. [ABSTRACT FROM AUTHOR]

Up to 17 GPa, the crystalline phases of N2 are characterized by pronounced orientational disorder, whereas the higher-pressure phases of molecular N2 are ordered. This raises the question about long-term relaxation of orientational disorder within the low- to intermediate-pressure regime. Here, this question is addressed by comparing synthetic with natural, chemically pure, solid N2 that resides as inclusions in diamonds at 300 K for about 108 years at pressures up to 11 GPa. It is shown that disorder prevails at 8.7 GPa, 300 K, where both synthetic and natural N2 assume the same structure. However, at 10.8 GPa, natural solid N2 exhibits monoclinic distortion and partial orientational ordering of the molecules, both of which are not observed in synthetic material. This difference is interpreted as the result of long-term structural relaxation. The ordering mechanism is examined and placed into the context of the δ- to ε-N2 transition. We present explanations for the absence of complete ordering of δ-N2. [ABSTRACT FROM AUTHOR]

Over four decades, the 3262.622(2) cm−1 band [Halonen and Duxbury, Chem. Phys. Lett. 118, 246–251 (1985)] of H2C=NH (methyleneimine or methanimine) has been cited as the ν1 NH stretch fundamental. In this article, the assignment is comprehensively reviewed for the first time, concluding that the band should instead be assigned to the CN stretching overtone 2ν4. The analysis of vibrational wavenumbers and transition dipole moments is guided by large basis set coupled-cluster anharmonic frequency calculations. A comparison with the vibrations of its perfluorinated analog (difluoromethanimine, F2C=NH) exemplifies that fc-CCSD(T)/ANO2 VPT2, as expected, is able to provide very accurate vibrational band centers for these semi-rigid molecules. As a by-product of the analysis, a significant reorientation of the ν1 transition dipole moment of methyleneimine by more than 100° away from the NH bond toward the nitrogen lone pair is found. MP2 fails to capture this effect, possibly due to a mild multireference character as suggested by a comparison with CCD, CCSD, and CCSD(T). [ABSTRACT FROM AUTHOR]

A monolayer of 4-nitrothiophenol adsorbed on an Au substrate was heated by illuminating the substrate with a 19 ps laser pulse of 532 nm wavelength. Within 91 ps, the temperature of the sample increased from room temperature by 113 K. Vibrational sum frequency spectroscopy was used to characterize the adsorption geometry of the molecules in the ordered domains in the monolayer film. Upon heating, the initially ordered monolayer largely lost its structure. While the molecules are initially tilted by about 50° with respect to the surface normal, the analysis indicates that the mean tilt angle increased to 80° with a spread for individual molecules of up to a tilt angle of 40° upon heating. The evolution of this loss of order lagged about 100 ps behind the temperature rise of the substrate. [ABSTRACT FROM AUTHOR]

Organic materials typically do not phosphoresce at room temperature because both intersystem crossing (ISC) and phosphorescence back to the electronic ground state are slow, compared to the nonradiative decay processes. A group of organic guest–host molecules breaks this rule. Their phosphorescence at room temperature can last seconds with a quantum efficiency of over 10%. This extraordinary phenomenon is investigated with comprehensive static and transient spectroscopic techniques. Time-resolved vibrational and fluorescence spectral results suggest that a singlet guest–host exciplex quickly forms after excitation. The formation of exciplex reduces the singlet–triplet energy gap and helps facilitate charge separation that can further diffuse into the host matrix. The heavy atoms (P or As) of the host molecule can also help enhance the spin orbital coupling of the guest molecule. Both boost the rate of ISC. After the singlet exciplex transforms into the triplet exciplex through the ISC process, UV–visible transient absorption spectroscopic measurements support that the triplet exciplex quickly transforms into the guest molecule triplet state that is at a lower energy level, thereby reducing the reverse ISC-induced triplet population loss. Finally, the long-lasting separated charges that diffused into the host matrix can diffuse back to the guest hole to form new triplets, and the dilution effect of the host molecules can effectively reduce the triplet quenching. All these factors contribute to the dramatic enhancement of phosphorescence at room temperature. [ABSTRACT FROM AUTHOR]

A method for the calculation of divergenceless, magnetically induced quantum mechanical current densities in molecules that approximates the exact current is presented. This was achieved by adding to the calculated conventional current density, i.e., a current that typically has a non-zero divergence, a corrective term that is the negative of the irrotational field of its Helmholtz decomposition. The solenoidal field of the decomposition is the divergence-free current density, which is still an approximation of the exact current but which now satisfies the continuity requirement regardless of the quality of the basis set. Based on calculations performed on several simple molecules (LiH, H2O, benzene, and zethrene), adopting different kinds of low-level theoretical approaches, clear improvements are observed in the correspondence of vortices, sources, and sinks for which the conventional current density shows a lack of continuity. A little improvement is also observed for the calculated diagonal components of the magnetizability tensor. [ABSTRACT FROM AUTHOR]

The physicochemical properties of molecules can be modulated through polariton formation under strong electromagnetic confinement. Here, we discuss the possibility of exploiting this phenomenon to increase the electron transfer rate at an electrode–electrolyte interface. Electron transfer theory under strong electromagnetic confinement can be extended to the electrode–electrolyte interface, and single-electron transfer reactions can be simulated using Gerischer's theory. Although single electron transfer in free space is well described using Marcus theory, the vacuum electric field can facilitate an additional electron transfer pathway via virtual photon excitation under cavity strong coupling conditions. Therefore, this binary reaction pathway for single electron transfer can yield a quasi-two-particle electron transfer process. This quantum behavior can dominate when the mode volume is small and when there are a large number of molecules in the vacuum electric field. Exploitation of polaritons in single electron transfer reactions can lead to enhanced electrochemical energy conversion systems. [ABSTRACT FROM AUTHOR]

Proton-transfer mechanisms and hydration states were investigated in chitin films possessing the functionality of fuel-cell electrolytes. The absolute hydration number per chitin molecule (N) as a function of relative humidity (RH) was determined from the OH stretching bands of H2O molecules, and the proton conductivity was found to enhance above N = 2 (80%RH). The FIR spectrum at 500–900 cm−1 for 20%RH (N < 1) together with first-principles calculations clearly shows that the w1 site has the same hydration strength as the w2 site. The molecular dynamics simulations for N = 2 demonstrate that H2O molecules with tiny fluctuations are localized on w1 and w2, and the hydrogen-bond (HB) network is formed via the CH2OH group of chitin molecules. Shrinkage of the O–O distance (dOO), which synchronizes with the barrier height, is required for proton transfer from H3O+ to adjacent CH2OH groups or H2O molecules. Nevertheless, dOO is hardly modulated for N = 2 because H2O molecules are strongly constrained on w1 and w2, and therefore, the transfer probability becomes small. For N = 3, novel HBs emerged between the additional H2O molecules broadly distributed on the w3 site and H2O molecules on w1 and w2. The transfer probability is enhanced because large fluctuations and diffusions in the whole H2O molecule yield large modulations of dOO. Consequently, long-range proton hopping is driven by the Zundel-type protonated hydrates in the water network. [ABSTRACT FROM AUTHOR]

The behavior of hydration water around familial Parkinson's disease linked mutants of α-synuclein may be linked to the early-onset of Parkinson's disease. For the first time, this study compares the local structure and dynamics of hydration water around different segments of some of the natural mutants of α-synuclein, i.e., E46K, G51D, A30P, and A53E, with that of the wild-type protein through explicit water MD simulations. The results show that the C-terminal segments of the fast aggregating mutants such as E46K and A30P are less exposed to water, while those of the slow aggregating ones such as A53E and G51D are more exposed to water relative to that of the wild-type protein. In addition, the water molecules are found to be more ordered around the C-terminal segment of the A53E and G51D mutants as compared to the wild-type protein. This is due to an increase in the overall charge of α-syn upon A53E and G51D mutations. The translational and rotational motions of water molecules in the hydration shell of the C-terminal segment of A53E and G51D mutants are found to be faster relative to that of the wild-type protein. This study validates the differential hydration environment around the C-terminal segment for the causative and protective mutants of α-synuclein. [ABSTRACT FROM AUTHOR]

Obtaining sub-chemical accuracy (1 kJ mol−1) for reaction energies of medium-sized gas-phase molecules is a longstanding challenge in the field of thermochemical modeling. The perturbative triples correction to coupled-cluster single double triple [CCSD(T)] constitutes an important component of all high-accuracy composite model chemistries that obtain this accuracy but can be a roadblock in the calculation of medium to large systems due to its O ( N 7 ) scaling, particularly in HEAT-like model chemistries that eschew separation of core and valence correlation. This study extends the work of Lesiuk [J. Chem. Phys. 156, 064103 (2022)] with new approximate methods and assesses the accuracy of five different approximations of (T) in the context of a subset of molecules selected from the W4-17 dataset. It is demonstrated that all of these approximate methods can achieve sub-0.1 kJ mol−1 accuracy with respect to canonical, density-fitted (T) contributions with a modest number of projectors. The approximation labeled Z ̃ T appears to offer the best trade-off between cost and accuracy and shows significant promise in an order-of-magnitude reduction in the computational cost of the CCSD(T) component of high-accuracy model chemistries. [ABSTRACT FROM AUTHOR]

In the conventional GW method, the three-point vertex function (Γ) is approximated to unity (Γ ∼ 1). Here, we developed an all-electron first-principles GWΓ method beyond a conventional GW method by considering a first-order three-point vertex function (Γ(1) = 1 + iGGW) in a one-electron self-energy operator. We applied the GWΓ method to simulate the binding energies (BEs) of B1s, C1s, N1s, O1s, and F1s for 19 small-sized molecules. Contrary to the one-shot GW method [or G0W0(LDA)], which underestimates the experimentally determined absolute BEs by about 3.7 eV for B1s, 5.1 eV for C1s, 6.9 eV for N1s, 7.8 eV for O1s, and 5.8 eV for F1s, the GWΓ method successfully reduces these errors by approximately 1–2 eV for all the elements studied here. Notably, the first-order three-point vertex corrections are more significant for heavier elements, following the order of F > O > N > C > B1s. Finally, the computational cost analysis revealed that one term in the GWΓ one-electron self-energy operator, despite being computationally intensive, contributes negligibly (< 0.1 eV) to the C1s, N1s, O1s, and F1s. [ABSTRACT FROM AUTHOR]

Nonadiabatic quantum dynamics are carried out to illustrate the photoionized spectrum of the cyanopropyne (CH3–C≡C–C≡N) as reported in recent experimental measurements [Lamarre et al., J. Mol. Spectrosc. 315, 206 (2015)]. A detailed electronic structure calculation is performed to analyze the topographical details of the first five ionized states, of which three are degenerate states ( X ̃ 2 E , B ̃ 2 E , and C ̃ 2 E) and two are non-degenerate states ( A ̃ 2 A 1 and D ̃ 2 A 1 ). The degenerate E states of the C3V symmetry molecule are prone to Jahn–Teller (JT) instability, and in addition, symmetry allowed A1 − E vibronic coupling, i.e., pseudo-Jahn–Teller (PJT), effects are expected to have a significant impact in the detailed vibronic structure of these electronic states. The JT splittings of X ̃ 2 E and B ̃ 2 E degenerate states are small, whereas it is quite large at three high frequencies in the C ̃ 2 E electronic states. The large energy separation of X ̃ 2 E from the other states and the non-zero PJT coupling of the B ̃ 2 E state with the close-lying A ̃ 2 A 1 state indicate the uncoupled nature of the X ̃ , A ̃ , and B ̃ vibronic bands of C4H3N. The intersection minima of B ̃ and C ̃ states with the D ̃ state nearly coincide with the energetic minimum of D ̃ state. Therefore, the PJT couplings among these states will lead to a strong vibronic interaction to shape the respective band structure. To completely understand the JT and PJT interactions in the photoionized spectrum of C4H3N, the vibronic coupling model Hamiltonian was constructed to perform nuclear dynamics studies for these electronic states. The vibrational progressions in each vibronic band are identified and compared with the available experimental data in the literature. The impacts of JT and PJT effects in the first five ionized states of cyanopropyne are investigated and discussed in detail. [ABSTRACT FROM AUTHOR]

The generation of cold molecules is an important topic in the field of cold atoms and molecules and has received relevant advanced research attention in ultracold chemistry, quantum computation, and quantum metrology. With a high atomic phase space density, optical dipole traps have been widely used to prepare, trap, and study cold molecules. In this work, Rb2 molecules were photoassociated in a magneto-optical trap to obtain a precise rovibrational spectrum, which provided accurate numerical references for the realization of multiple frequency photoassociation. By meeting the harsh requirements of photoassociation in optical dipole traps, the cold molecule photoassociation process was well explored, and different photoassociation resonances were simultaneously addressed in a single optical dipole trap. This method can be universally extended to simultaneously photoassociate cold molecules with different internal states or atomic species in a single optical dipole trap, thus advancing generous cold molecule studies such as cold molecule collision dynamics. [ABSTRACT FROM AUTHOR]

Second Harmonic Scattering (SHS) is a suitable technique to investigate the orientational correlations between molecules. This article explores the organization of different dye molecules adsorbed within the hydrophobic porosity of a hybrid organic–inorganic nanotube. Experimental polarization resolved SHS measurements highlight different orientational orders ranking from highly ordered and rigid organizations to disordered assemblies. Microscopic models of assemblies inside the pores are presented and discussed in the context of orientational correlation between the dye molecules. This work shows that the degree of order in the nanotube cavity follows the molecule's affinity within the porosity. [ABSTRACT FROM AUTHOR]

Investigating molecular excitation induced by collisions requires the prior determination of accurate analytical potential energy surfaces for the colliding partners. For carbon-chain molecules, such as cyanopolyynes, this has been a longstanding challenge, resulting in the absence of rate coefficients for HC5N, HC7N, HC9N, and others, induced by collisions with He. To overcome this bottleneck, we introduce a new approach: the Radial Angular Network with Gradual Expansion (RANGE). This method jointly connects the construction of ab initio interaction potentials with the determination of their analytical forms. We use the HC3N–He molecular complex as a reference to assess the reliability of our method, given that its analytical potential has been derived using various methods. Additionally, we apply the RANGE approach to construct the analytical representation of the interaction potential for HC5N–He and HC7N–He. The analysis of the analytical potentials reveals three systematic trends: (i) the anisotropy increases with the length of the carbon chain, (ii) the number of local minima correlates with the number of carbon atoms, and (iii) the shallowest local minimum is consistently located at ∼30 cm−1 below the dissociation limit of the complex. Using the time-independent quantum mechanical close-coupling formalism, we briefly estimate the propensity rules governing the excitation of HC3N, HC5N, and HC7N induced by collisions with He. Consequently, the three collisional systems exhibit the same propensity rule, favoring Δj = 2 transitions. [ABSTRACT FROM AUTHOR]

We apply the analytically solvable model of two electrons in two orbitals to diradical molecules, characterized by two unpaired electrons. The effect of doubly occupied and empty orbitals is taken into account by means of random phase approximation (RPA). We show that in the static limit, the direct RPA leads to the renormalization of the parameters of the two-orbital model. We test our model by comparing its predictions for singlet–triplet splitting with the results of several multi-reference methods for a set of thirteen molecules. We find that for this set, the static RPA results are close to those of the NEVPT2 method with two orbitals and two electrons in the active space. [ABSTRACT FROM AUTHOR]

We derive an analytic expression of the non-equilibrium Fermi's golden rule (NE-FGR) expression for a Holstein–Tavis–Cumming Hamiltonian, a universal model for many molecules collectively coupled to the optical cavity. These NE-FGR expressions capture the full-time-dependent behavior of the rate constant for transitions from polariton states to dark states. The rate is shown to be reduced to the well-known frequency domain-based equilibrium Fermi's golden rule (E-FGR) expression in the equilibrium and collective limit and is shown to retain the same scaling with the number of sites in non-equilibrium and non-collective cases. We use these NE-FGR to perform population dynamics with a time-non-local and time-local quantum master equation and obtain accurate population dynamics from the initially occupied upper or lower polariton states. Furthermore, NE-FGR significantly improves the accuracy of the population dynamics when starting from the lower polariton compared to the E-FGR theory, highlighting the importance of the non-Markovian behavior and the short-time transient behavior in the transition rate constant. [ABSTRACT FROM AUTHOR]

Intrinsically disordered proteins (IDPs) are prevalent participants in liquid–liquid phase separation due to their inherent potential for promoting multivalent binding. Understanding the underlying mechanisms of phase separation is challenging, as phase separation is a complex process, involving numerous molecules and various types of interactions. Here, we used a simplified coarse-grained model of IDPs to investigate the thermodynamic stability of the dense phase, conformational properties of IDPs, chain dynamics, and kinetic rates of forming condensates. We focused on the IDP system, in which the oppositely charged IDPs are maximally segregated, inherently possessing a high propensity for phase separation. By varying interaction strengths, salt concentrations, and temperatures, we observed that IDPs in the dense phase exhibited highly conserved conformational characteristics, which are more extended than those in the dilute phase. Although the chain motions and global conformational dynamics of IDPs in the condensates are slow due to the high viscosity, local chain flexibility at the short timescales is largely preserved with respect to that at the free state. Strikingly, we observed a non-monotonic relationship between interaction strengths and kinetic rates for forming condensates. As strong interactions of IDPs result in high stable condensates, our results suggest that the thermodynamics and kinetics of phase separation are decoupled and optimized by the speed-stability balance through underlying molecular interactions. Our findings contribute to the molecular-level understanding of phase separation and offer valuable insights into the developments of engineering strategies for precise regulation of biomolecular condensates. [ABSTRACT FROM AUTHOR]

In this work, the adsorption structure of deuterated water on the stepped platinum surface is studied under an ultra-high vacuum by using heterodyne-detected sum-frequency generation spectroscopy. On a pristine Pt(553), D2O molecules adsorbed at the step sites act as hydrogen bond (H-bond) donors to the adjacent terrace sites. This ensures the net D-down orientation at the terrace sites away from the steps. In particular, the pre-adsorption of oxygen atoms at the step sites significantly alters the D-down configuration. The oxygen pre-adsorption leads to a spontaneous dissociation of the post-adsorbed water molecules at the step to form hydroxyl (OD) species. Since the hydroxyl at the step acts as a strong H-bond acceptor, D2O at the terrace no longer maintains the D-down configuration and adopts flat-lying configurations, significantly reducing the number of D-down molecules at the terrace. Density-functional theoretical calculations support these pictures. This work demonstrates the critical role of steps in controlling the net orientation of the interfacial water and provides an important reference for future considerations of the reactions at electrochemical interfaces. [ABSTRACT FROM AUTHOR]

We present a comprehensive computational study describing the excited state dynamics and consequent photostability of amino-cyclohexenone (ACyO), the central template of mycosporine systems, widely recognized for their photoprotection of aquatic species. Photoexcitation to the first excited electronic state (S1, 1nπ*) of ACyO is considered an optically dark transition, while photoexcitation to the second excited electronic state (S21ππ*) is an optically bright 1ππ* transition and largely responsible for UV absorption properties of this molecule. We show that following initial photoexcitation to S2, ACyO relaxes via two competing deactivation mechanisms, each mediated by an S1/S0 conical intersection, which directs the excited state population to the electronic ground state (S0). Our ab initio computational results are supported with nonadiabatic dynamics simulation results, yielding an excited state lifetime of ∼280 fs for this system in vacuo. These results explain the inherent photostability of this core structure, commonplace in a wide range of microorganisms. [ABSTRACT FROM AUTHOR]

Motivated by experimental reports on chirality induced spin selectivity, we investigate a minimal model that allows us to calculate the charge and spin conductances through helical molecules analytically. The spin–orbit interaction is assumed to be non-vanishing on the molecule and negligible in the reservoirs (leads). The band structure of the molecule features four helical modes with spin-momentum locking that are analogous of edge-currents in the quantum spin Hall effect. While charge is conserved and therefore the charge current is independent of where it is measured—reservoirs or molecule—our detailed calculations reveal that the spin currents in the left and right leads are equal in magnitudes but with opposite signs (in linear response). We predict that transport currents flowing through helical molecules are accompanied by a spin accumulation in the contact region with the same magnetization direction for source and drain. Furthermore, we predict that the spin-conductance can be extracted directly from measuring the (quasi-static) spin accumulation—rather than the spin current itself, which is very challenging to obtain experimentally. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

For floppy molecules showing internal rotations and/or large amplitude motions, curvilinear internal coordinates are known to be superior to rectilinear normal coordinates within vibrational structure calculations. Due to the myriad definitions of internal coordinates, automated and efficient potential energy surface generators necessitate a high degree of flexibility, supporting the properties arising from these coordinates. Within this work, an approach to deal with these challenges is presented, including key elements, such as the selection of appropriate fit functions, the exploitation of symmetry, the positioning of grid points, or elongation limits for different coordinates. These elements are tested for five definitions of curvilinear coordinates, with three of them being generated in an automated manner. Calculations for semi-rigid molecules, namely H2O, H2CO, CH2F2, and H2CNH, demonstrate the general functionality of the implemented algorithms. Additional calculations for the HOPO molecule highlight the benefits of these curvilinear coordinates for systems with large amplitude motions. This new implementation allowed us to compare the performance of these different coordinate systems with respect to the convergence of the underlying expansion of the potential energy surface and subsequent vibrational configuration interaction calculations. [ABSTRACT FROM AUTHOR]

RNA pseudoknots are RNA molecules with specialized three-dimensional structures that play important roles in various biological processes. To understand the functions and mechanisms of pseudoknots, it is essential to elucidate their structures and folding pathways. The most fundamental step in RNA folding is the opening and closing of a base pair. The effect of flexible loops on the base pair in pseudoknots remains unclear. In this work, we use molecular dynamics simulations and Markov state model to study the configurations, thermodynamic and kinetic of single base pair in pseudoknots. We find that the presence of the loop leads to a trap state. In addition, the rate-limiting step for the formation of base pair is the disruption of the trap state, rather than the open state to the closed state, which is quite different from the previous studies on non-pseudoknot RNA. For the thermodynamic parameters in pseudoknots, we find that the entropy difference upon opening the base pair between this simulation and the nearest-neighbor model results from the different entropy of different lengths of loop in solution. The thermodynamic parameters of the stack in pseudoknot are close to the nearest-neighbor parameters. The bases on the loop have different distribution patterns in different states, and the slow transition states of the loop are determined by the orientation of the bases. [ABSTRACT FROM AUTHOR]

Sizable glass formers feature numerous unique properties and potential applications, but many questions regarding their glass transition dynamics have not been resolved yet. Here, we have analyzed structural relaxation times measured as a function of temperature and pressure in combination with the equation of state obtained from pressure–volume–temperature measurements. Despite evidence from previous dielectric studies indicating a remarkable sensitivity of supercooled dynamics to compression, and contrary to intuition, our results demonstrated the proof for the almost equivalent importance of thermal energy and free volume fluctuations in controlling reorientation dynamics of sizable molecules. The found scaling exponent γ = 3.0 and Ev/Ep ratio of 0.6 were typical for glass-forming materials with relaxation dynamics determined by both effects with a minor advantage of thermal fluctuations involvement. It shows that the high values of key parameters characterizing the sensitivity of the glass transition dynamics to pressure changes, i.e., activation volume ΔV and dTg/dP, are not a valid premise for a remarkable contribution of volume to glass transition dynamics. [ABSTRACT FROM AUTHOR]

In this work, we study the energy flow through anharmonic coupling of vibrational modes after excitation of gas-phase fluorobenzene with a multi-THz pump. We show that to predict the efficiency of anharmonic energy transfer, simple models that only include the anharmonic coupling coefficients and motion of modes at their resonant frequency are not adequate. The full motion of each mode is needed, including the time while the mode is being driven by the pump pulse, because all the frequencies present in the multi-THz pump contribute to the excitation of the non-resonantly excited vibrational modes. Additionally, the model gives us the insight that modes with either A1 or B2 symmetry are more actively involved in anharmonic coupling because these modes have more symmetry-allowed energy transfer pathways. [ABSTRACT FROM AUTHOR]

Fully relativistic calculations, primarily at the 4-component coupled-cluster singles and doubles with perturbative triples [CCSD(T)] level of theory with the Dirac–Coulomb (DC) Hamiltonian, have been carried out for the superheavy (E125)F molecule using large Gaussian basis sets. The electronic ground state is determined to have an [Og]8s25g16f3 configuration on E125 with an Ω = 6 ground state and an 8p electron largely donated to F. A Mulliken population analysis indicates that the ground state is mainly ionic with a partial charge of +0.79 on E125 and a single sigma bond involving the F 2p and E125 8p spinors. The occupied g spinor is not involved in the bonding. With the largest basis set used in this work, the (0 K) dissociation energy was calculated at the DC-CCSD(T) level of theory to be 7.02 eV. Analogous calculations were also carried out for the E125 atom, both the neutral and its cation. The lowest energy electron configuration of E125+, [Og] 8 s 1 / 2 2 5 g 7 / 2 1 6 f 5 / 2 3 with a J = 6 ground state, was found to be similar to that in (E125)F, while the neutral E125 atom has an [Og] 8 s 1 / 2 2 5 g 7 / 2 1 6 f 5 / 2 2 7 d 3 / 2 1 8 p 1 / 2 1 ground state electron configuration with a J = 17/2 ground state. The ionization energy (IE) of E125 is reported for the first time and is calculated to be 4.70 eV at the DC-CCSD(T) level of theory. Non-relativistic calculations were also carried out on the E125 atom and the (E125)F molecule. The non-relativistic ground state of the E125 atom was calculated to have a 5g5 ground state with an IE of just 3.4 eV. The net effect of relativity on (E125)F is to stabilize its bonding. [ABSTRACT FROM AUTHOR]

A summary of the development of Monte Carlo statistical mechanics simulations for the computation of free energies of hydration of organic molecules is followed by presentation of results with the latest version of the optimized potentials for liquid simulations–all atom force field and the TIP4P water model. Scaling of the Lennard-Jones interactions between water, oxygen, and carbon atoms by a factor of 1.25 is found to improve the accuracy of free energies of hydration for 50 prototypical organic molecules from a mean unsigned error of 1.0–1.2 to 0.4 kcal/mol. [ABSTRACT FROM AUTHOR]

Electronic friction and Langevin dynamics is a popular mixed quantum–classical method for simulating the nonadiabatic dynamics of molecules interacting with metal surfaces, as it can be computationally more efficient than fully quantum approaches. In this work, we extend the theory of electronic friction within the hierarchical equations of motion formalism to models with a position-dependent metal–molecule coupling. We show that the addition of a position-dependent metal–molecule coupling adds new contributions to the electronic friction and other forces, which are highly relevant for many physical processes. Our expressions for the electronic forces within the Langevin equation are valid both in and out of equilibrium and for molecular models containing strong interactions. We demonstrate the approach by applying it to different models of interest. [ABSTRACT FROM AUTHOR]

The chemiresistive effect of an oxide significantly influences its electrical properties, which depend greatly on the interactions between the ambient gas molecules and the solid surface, including the gas adsorption and charge transfer still challenging to be clarified. In this work, we investigate the chemiresistive effect of the p-type delafossite CuScO2 microsheets by comparing their responses to various gaseous alcohols, which increase with an approximately linear relationship with the length of straight carbon chains from methanol to n-hexanol. A new mechanism is proposed to elucidate such a dramatic trend of observed chemiresistive change based on the first-principles calculations and test results. The increasing carbon chain length modulates the adsorption configuration and provides supplementary routes for electron transfer, which is assumed to account for the observed chemiresistive effect. This work may provide a novel perspective for the investigation and development of more advanced functional oxides for electrical applications. [ABSTRACT FROM AUTHOR]

We investigate an efficient spatial enantioseparation method of chiral molecules in cyclic three-level systems coupled with three optical fields using optically induced forces. When the overall phase differs by π between two enantiomers, significant variations in the magnitude and direction of the optically induced forces are observed. The manipulation of the center of mass of chiral molecules in optical fields can be achieved through the induced gauge force, primarily generated from the variations in the chirality-dependent scalar potentials created by the three inhomogeneous laser fields. By appropriately configuring the system, we can completely separate the slow spatial and fast inner dynamics, making instantaneous eigenstates of the inner Hamiltonian independent of the transverse profiles of the laser beams. Compared to previous methods, which required adiabatic conditions to be satisfied, the proposed method overcomes the limitations of the adiabatic approximation by utilizing a specific system configuration. This allows for increased flexibility in the transverse profiles of the laser beams and relaxes the constraints on the velocity of chiral molecules, leading to significantly greater spatial separations achievable across a broader range of parameters. [ABSTRACT FROM AUTHOR]

We investigate the vertical electron attachment energy (VAE) of 1-methyl-4-nitroimidazole, a model radiosensitizer, employing quantum mechanics/molecular mechanics (QM/MM) and QM/polarized continuum (QM/PCM) solvation models. We considered the solvent-excluded surface (QM/PCM-SES) and Van der Waals (QM/PCM-VDW) cavities within the PCM framework, the electrostatic embedding QM/MM (EE-QM/MM) model, and the self-consistent sequential QM/MM polarizable electrostatic embedding (scPEE-S-QM/MM) model. Due to slow VAE convergence concerning the number of QM solvent molecules, full QM calculations prove inefficient. Ensemble averages in these calculations do not align with VAEs computed for the representative solute–solvent configuration. QM/MM and QM/PCM calculations show agreement with each other for sufficiently large QM regions, although the QM/PCM-VDW model exhibits artifacts linked to the cavity. QM/MM models demonstrate good agreement between ensemble averages and VAEs calculated with the representative configuration. Notably, the VAE computed with the scPEE-S-QM/MM model achieves faster convergence concerning the number of QM water molecules compared to the EE-QM/MM model, attributed to enhanced efficiency from MM charge polarization in the scPEE-S-QM/MM approach. This emphasizes the importance of QM/classical models with accurate solute–solvent and solvent–solvent mutual polarization for obtaining converged VAEs at a reasonable computational cost. The full-QM approach is very inefficient, while the microsolvation model is inaccurate. Computational savings in QM/MM models result from electrostatic embedding and the representative configuration, with the scPEE-S-QM/MM approach emerging as an efficient tool for describing bulk-solvated anions within the QM/MM framework. Its potential extends to improving transient anion state descriptions in biomolecules and radiosensitizers, especially given the frequent employment of microsolvation models. [ABSTRACT FROM AUTHOR]

We present a four-component relativistic unitary coupled cluster method for atoms and molecules. We have used commutator-based non-perturbative approximation using the "Bernoulli expansion" to derive an approximation to the relativistic unitary coupled cluster method. The performance of the full quadratic unitary coupled-cluster singles and doubles method (qUCCSD), as well as a perturbative approximation variant (UCC3), has been reported for both energies and properties. It can be seen that both methods give results comparable to those of the standard relativistic coupled cluster method. The qUCCSD method shows better agreement with experimental results due to the better inclusion of relaxation effects. The relativistic UCC3 and qUCCSD methods can simulate the spin-forbidden transition with easy access to transition properties. A natural spinor-based scheme to reduce the computational cost of relativistic UCC3 and qUCCSD methods has been discussed. [ABSTRACT FROM AUTHOR]

The theory of polymer dynamics describes the intermediate scattering function for a polymer molecule in terms of relaxation modes defined by normal coordinates for the corresponding coarse-grained model. However, due to the difficulty of defining the normal coordinates for arbitrary polymer molecules, it is generally challenging to express the intermediate scattering function for a polymer molecule in terms of relaxation modes. To overcome this challenge, we propose a general method to calculate the intermediate scattering function for a polymer molecule on the basis of a relaxation mode analysis approach [Takano and Miyashita, J. Phys. Soc. Jpn. 64, 3688 (1995)]. In the proposed method, relaxation modes defined by eigenfunctions in a Markov process are evaluated on the basis of the simulation results for a polymer molecule and used to calculate the intermediate scattering function for that molecule. To demonstrate the effectiveness of the present method, we simulate the dynamics of a linear polymer molecule in a dilute solution and apply it to the calculation of the intermediate scattering function for the polymer molecule. The evaluation results regarding the relaxation modes reasonably describe the intermediate scattering function on the length scale of the radius of gyration of the polymer molecule. Accordingly, we examine the contributions of the pure relaxation and oscillatory relaxation processes to the entire intermediate scattering function. [ABSTRACT FROM AUTHOR]

Cholesterol (Chol) plays a crucial role in shaping the intricate physicochemical attributes of biomembranes, exerting a considerable influence on water molecules proximal to the membrane interface. In this study, we conducted molecular dynamics simulations on the bilayers of two lipid species, dipalmitoylphosphatidylcholine (DPPC) and palmitoyl sphingomyelin; they are distinct with respect to the structures of the hydrogen-bond (H-bond) acceptors. Our investigation focuses on the dynamic properties and H-bonds of water molecules in the lipid-membrane systems, with a particular emphasis on the influence of Chol at varying temperatures. Notably, in the gel phase at 303 K, the presence of Chol extends the lifetimes of H-bonds of the oxygen atoms acting as H-bond acceptors within DPPC with water molecules by a factor of 1.5–2.5. In the liquid-crystalline phase at 323 K, on the other hand, H-bonding dynamics with lipid membranes remain largely unaffected by Chol. This observed shift in H-bonding states serves as a crucial key to unraveling the subtle control mechanisms governing water dynamics in lipid-membrane systems. [ABSTRACT FROM AUTHOR]

Magnetometer cell wall coat molecules play an important role in preserving the lifetime of pumped alkali metal atoms for use in magnetometers that are capable of measuring very small magnetic fields. The goal of this study is to help rationalize the design of the cell coat molecules. Rubidium-87 is studied in terms of its interaction with three template cell coat molecules: ethane, ethene, and methyltrichlorosilane (MeTS). Ab initio electronic structure methods are applied to investigate the effect that the coat molecules have on the 2S ground state and 2P excited state of 87Rb. We find that, from the ab initio results, the three template molecules have differing effects, with MeTS having the largest effect on the ground state and ethane or ethene having the largest effect on the non-degenerate excited states. [ABSTRACT FROM AUTHOR]

We show that optimal control of the electron dynamics is able to prepare molecular ground states, within chemical accuracy, with evolution times approaching the bounds imposed by quantum mechanics. We propose a specific parameterization of the molecular evolution only in terms of interaction already present in the molecular Hamiltonian. Thus, the proposed method solely utilizes quantum simulation routines, retaining their favorable scalings. Due to the intimate relationships between variational quantum algorithms and optimal control, we compare, when possible, our results with state-of-the-art methods in the literature. We found that the number of parameters needed to reach chemical accuracy and algorithmic scaling is in line with compact adaptive strategies to build variational Ansätze. The algorithm, which is also suitable for quantum simulators, is implemented by emulating a digital quantum processor (up to 16 qubits) and tested on different molecules and geometries spanning different degrees of electron correlation. [ABSTRACT FROM AUTHOR]

The control of movement and orientation of gas-phase molecules has become the focus of many research areas in molecular physics. Here, ND3 molecules are polarized in a segmented, curved electrostatic guide and adiabatically aligned inside a rotatable mass spectrometer (MS). Alignment is probed by photoionization using a linearly polarized laser. Rotation of the polarization at fixed MS orientation has the same effect as the rotation of the MS at fixed polarization, proving that the molecular alignment adiabatically follows the MS axis. Polarization-dependent ion signals reveal state-specific populations and allow for a quantification of the aligned sample in the space-fixed reference frame. [ABSTRACT FROM AUTHOR]

Dimensions and molecular structures play pivotal roles in the principle of heat conduction. The dimensional characteristics of a solution within nanoscale systems depend on the degrees of confinement. However, the influence of such variations on heat transfer remains inadequately understood. Here, we perform quasi-one-dimensional non-equilibrium molecular dynamics simulations to calculate the thermal conductivity of water molecules confined in carbon nanotubes. The structure of water molecules is determined depending on the nanotube radius, forming a single-file, a single-layer, and a double-layer structure, corresponding to an increasing radius order. We reveal that the thermal conductivity of liquid water has a sublinear dependency on nanotube length exclusively when water molecules form a single file. A stronger confinement leads to behavioral and structural characteristics closely resembling a one-dimensional nature. Moreover, single-layer-structured water molecules exhibit enhanced thermal conductivity. We elucidate that this is due to the increase in the local water density and the absence of transitions to another layer, which typically occurs in systems with double-layer water structures within relatively large radius nanotubes. [ABSTRACT FROM AUTHOR]

A novel mixed quantum–classical approach to simulating nonadiabatic dynamics of molecules at metal surfaces is presented. The method combines the numerically exact hierarchical equations of motion approach for the quantum electronic degrees of freedom with Langevin dynamics for the classical degrees of freedom, namely, low-frequency vibrational modes within the molecule. The approach extends previous mixed quantum–classical methods based on Langevin equations to models containing strong electron–electron or quantum electronic–vibrational interactions, while maintaining a nonperturbative and non-Markovian treatment of the molecule–metal coupling. To demonstrate the approach, nonequilibrium transport observables are calculated for a molecular nanojunction containing strong interactions. [ABSTRACT FROM AUTHOR]

We have determined the bond dissociation energy of O2 by measuring fully state-to-state resolved threshold fragment yield spectra in the XUV energy region, O 2 X 3 Σ g − , N ″ , J ″ → O ( P J 3 ) + O ( S 1 o 3 ) / O ( S 2 o 5 ). Our results have yielded a bond dissociation energy value of 41 269.19 ± 0.10 cm−1, which is consistent with previous measurements but exhibits a significantly lower uncertainty, approximately five times smaller. It is noteworthy that this study is the first to simultaneously achieve fine structure state resolution for the parent O2 molecule and spin–orbit state resolution for the O(3PJ) fragments in the measurement of O2 bond dissociation energy. As a result, our findings have established a solid foundation for the obtained data. [ABSTRACT FROM AUTHOR]

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

In the rich ice polymorphism landscape, ice XVII, metastable at ambient pressure and at temperatures below 130 K, is surely one of the most interesting from both fundamental and technological perspectives due to its porosity, i.e., its capability to repeatedly absorb and desorb molecular hydrogen by dosing the gas at pressures even below the ambient one. Here, owing to this exceptional key feature, we investigate the roto-vibrational dynamics of the H2 molecules trapped in the fully deuterated ice XVII structure. Making use of the high-resolution and brilliance of the TOSCA neutron vibrational spectrometer, combined with high-resolution Raman data, we are able to efficiently distinguish the center-of-mass translational bands from the rotational ones and to study them as a function of the guest filling of the ice structure, unraveling a peculiar behavior for the confined particle in a low-dimensional system. Moreover, we also report the study of the microscopic dynamics of confined nitrogen and oxygen, which are the most abundant molecular species in the atmosphere and are of paramount interest for technological applications. Finally, we show that the ice XVII porosity is a unique feature, especially in the low pressure regime, within the emptied-hydrate phases discovered to date. [ABSTRACT FROM AUTHOR]