Intramolecular Contributions Research Articles

Equipartitioning of Molecular Degrees of Freedom in MD Simulations of Gaseous Systems via an Advanced Thermostatization Strategy.

This work introduces a dedicated thermostatization strategy for molecular dynamics simulations of gaseous systems. The proposed thermostat is based on the stochastic canonical velocity rescaling approach by Bussi and co-workers and is capable of ensuring an equal distribution of the kinetic energy among the translational, rotational, and vibrational degrees of freedom. The outlined framework ensures the correct treatment of the kinetic energy in gaseous systems, which is typically not the case in standard approaches due to the limited number of collisions between particles associated with a large free mean path. Additionally, an efficient strategy to effectively correct for intramolecular contributions to the virial in quantum mechanical simulations is presented. The equipartitioning thermostat was successfully tested by the determination of pV diagrams for carbon dioxide and methane at the density functional tight binding level of theory. The results unequivocally demonstrate that the equipartitioning thermostat can effectively achieve an equal distribution of the kinetic energy among the different degrees of freedom, thereby ensuring correct pressure in gaseous systems. Furthermore, RDF calculations show the capability of the proposed method to accurately depict the structure of gaseous systems, as well as enable an adequate treatment of gas molecules under confinement, as exemplified by an MD simulation of (CO2)50@MOF-5.

Intramolecular Polarization Contributions to the pKa's of Carboxylic Acids Through the Chain Length Dependence of Vibrational Tag-Shifts in Cryogenically Cooled Pyridinium-(CH2)n-COOH (n = 1-7) Cations.

The pKa's of acids are known to depend on the ionic strength of an electrolyte solution, an effect that qualitatively results from electrostatic interactions of the acid and conjugate base with proximal ions. Here, we explore an intramolecular variation on this theme in which a carboxylic acid group is tethered to a pyridinium cationic charge center with increasingly long alkyl linkages in the series Py+-(CH2)n-COOH, with n = 1-7. The effective acidities of the carboxylic acid group in the isolated cations are determined by recording the red-shifts in the frequencies of the acid OH stretches upon attachment to D2 and N2 molecules, measured by using cryogenic ion spectroscopy. The short chains indeed lead to substantial increases in acidity, with the effect falling off in the range of n = 4-5. The response of the CO stretch on the acid head group is surprisingly strong and, in contrast to the expected red shift of the OH, displays a blue shift as the chain length is reduced. Electronic structure calculations recover these trends and indicate that the proximal cationic charge center acts to draw electron density away from the acid C═O bond. This acts to blue-shift the CO stretch while weakening the C-C bond that attaches the head group to the chain.

Electron impact resonances of uracil in an aqueous environment from anion photoelectron imaging

The effect that solvation has on electron attachment to uracil, U, was studied by probing the electronic resonances of the uracil radical anion, U−, in gas-phase water clusters, U−(H2O) n , using photoelectron imaging across a range of photon energies. Specifically, the π 3* shape resonance was probed in detail and the spectral signatures following excitation to this resonance are considered. Several new methods for analysis are provided to capture the different actions of the resonance on the photoelectron emission, which in turn provide insight into the location of the π 3* resonance and its subsequent dynamics. The effect of solvation on each action observed through the photoelectron emission is studied for n ⩽ 10. We find that the actions—be they related to statistical emission, prompt autodetachment, or the photoelectron angular distributions—all become less sensitive as the cluster size increases, suggesting that their use for very large clusters may be limited. Additionally, we consider the correlation between electron detachment from the anion, as probed in the experiments, and electron attachment to the neutral. Specifically, they are linked through the reorganisation energy in a linear response picture and we show how the cluster approach developed here allows one to decompose the total reorganisation energy into intramolecular (associated with the anion to neutral geometry change in U) and intermolecular (associated with the change in hydration sphere) contributions. For U in a bulk aqueous environment, we find that the total reorganisation energy, λ ∼ 1.2 eV, shows equal contributions from both intra- and intermolecular changes.

Prediction of aqueous solubility of a strongly soluble solute from molecular simulation.

The prediction of solubilities of compounds by means of molecular simulation has been receiving increasing attention due to the key role played by solubility in countless applications. We have predicted the aqueous solubility of urea at 300K from chemical potential calculations for two urea model combinations: Özpinar/TIP3P and Hölzl/(TIP4P/2005). The methodology assumes that the intramolecular contribution of the urea molecule to the chemical potentials is identical in the crystal and in solution and, hence, cancels out. In parallel to the chemical potential calculations, we also performed direct coexistence simulations of a urea crystal slab in contact with urea-water solutions with the aim to identify upper and lower bounds to the solubility value using an independent route. The chemical potential approach yielded similar solubilities for both urea models, despite the actual chemical potential values showing a significant dependence on the force field. The predicted solubilities for the two models were 0.013-0.018 (Özpınar) and 0.008-0.012 (Hölzl) mole fraction, which are an order of magnitude lower than the experimental solubility that lies in a range of 0.125-0.216 mole fraction. The direct coexistence solubility bounds were relatively wide and did not encompass the chemical potential based solubilities, although the latter were close to the lower bound values.

Reversible Pressure-Magnetic Modulation in a Tetrathiafulvalene-Based Dyad Piezochromic Dysprosium Single-Molecule Magnet.

The extreme sensitivity of trivalent lanthanide ions to crystal field variations led to the emergence of single-molecule magnetic switching under various stimuli. The use of pressure as an external stimulus instead of classic light irradiation, oxidation or any chemical reactions allows a fine tuning of the magnetic modulation. Here the well-known pure isotopically enriched [162 Dy(tta)3 (L)]⋅C6 H14 (162 Dy) Single-Molecule Magnet (SMM) (tta- =2-2-thenoyltrifluoroacetonate and L=4,5-bis(propylthio)-tetrathiafulvalene-2-(2-pyridyl)benzimidazole-methyl-2-pyridine) was experimentally investigated by single-crystal diffraction and squid magnetometry under high applied pressures. Both reversible piezochromic properties and pressure modulation of the slow magnetic relaxation behavior were demonstrated and supported by ab initio calculations. The magnetic study of the diluted sample [162 Dy0.05 Y0.95 (tta)3 (L)]⋅C6 H14 (162 Dy@Y) indicated that variations in the electronic structure have mainly intermolecular origin with weak intramolecular contribution. Quantitative magnetic interpretation concludes to a deterioration of the Orbach process for the benefit of both Raman and QTM mechanisms under applied pressure.

Theoretical Insights into the Optical and Excited State Properties of Donor–Phenyl Bridge–Acceptor Containing Through-Space Charge Transfer Molecules

A comparative new strategy to enhance thermally activated delayed fluorescence (TADF) of through-space charge transfer (CT) molecules in organic light-emitting diodes (OLEDs) is investigated. Generally, TADF molecules adopt a twisted donor and acceptor structure to get a sufficiently small ΔEST and a higher value of the spin-orbit coupling matrix element (SOCME). However, molecules containing donor-phenyl bridge-acceptor (D-p-A) units and featuring π-stacked architectures have intramolecular CT contribution through space and exhibit high TADF efficiency. We have explored the insights into the TADF mechanism in D-p-A molecules using the density functional theory (DFT) and time-dependent DFT methods. The calculated optical absorption and ΔEST values are found to be in good agreement with available experimental data. Interestingly, we found the origin of the SOCME to be the twisted orientation of the donor and bridge moieties. Also, we predicted similar molecules with enhanced OLED efficiency with different substitutions.

Intermolecular contributions, filtration effects and signal composition of SIFTER (single-frequency technique for refocusing).

To characterize structure and molecular order in the nanometre range, distances between electron spins and their distributions can be measured via dipolar spin-spin interactions by different pulsed electron paramagnetic resonance experiments. Here, for the single-frequency technique for refocusing dipolar couplings (SIFTER), the buildup of dipolar modulation signal and intermolecular contributions is analysed for a uniform random distribution of monoradicals and biradicals in frozen glassy solvent by using the product operator formalism for electron spin . A dipolar oscillation artefact appearing at both ends of the SIFTER time trace is predicted, which originates from the weak coherence transfer between biradicals. The relative intensity of this artefact is predicted to be temperature independent but to increase with the spin concentration in the sample. Different compositions of the intermolecular background are predicted in the case of biradicals and in the case of monoradicals. Our theoretical account suggests that the appropriate procedure of extracting the intramolecular dipolar contribution (form factor) requires fitting and subtracting the unmodulated part, followed by division by an intermolecular background function that is different in shape. This scheme differs from the previously used heuristic background division approach. We compare our theoretical derivations to experimental SIFTER traces for nitroxide and trityl monoradicals and biradicals. Our analysis demonstrates a good qualitative match with the proposed theoretical description. The resulting perspectives for a quantitative analysis of SIFTER data are discussed.

The effect of spin polarization on double electron-electron resonance (DEER) spectroscopy.

Double electron-electron resonance (DEER) spectroscopy measures the distribution of distances between two electron spins in the nanometer range, often on doubly spin-labeled proteins, via the modulation of a refocused spin echo by the dipolar interaction between the spins. DEER is commonly conducted under conditions where the polarization of the spins is small. Here, we examine the DEER signal under conditions of high spin polarization, thermally obtainable at low temperatures and high magnetic fields, and show that the signal acquires a polarization-dependent out-of-phase component both for the intramolecular and intermolecular contributions. For the latter, this corresponds to a phase shift of the spin echo that is linear in the pump pulse position. We derive a compact analytical form of this phase shift and show experimental measurements using monoradical and biradical nitroxides at several fields and temperatures. The effect highlights a novel aspect of the fundamental spin physics underlying DEER spectroscopy.

Vibrational Dynamics of the Intramolecular H-Bond in Acetylacetone Investigated with Transient and 2D IR Spectroscopy.

Acetylacetone (AcAc) has proven to be a fruitful but highly challenging model system for the experimental and computational interrogation of strong intramolecular hydrogen bonds. Key questions remain, however, regarding the identity of the minimum-energy structure of AcAc and the dynamics of intramolecular proton transfer. Here, we investigate the OH/OD stretch and bend regions of the enol tautomer of AcAc and its deuterated isotopologue with transient absorption and 2D IR spectroscopy. The OH bend region reveals a single dominant diagonal transition near 1625 cm-1 with intense cross peaks to lower-frequency modes, demonstrating highly mixed fingerprint transitions that contain OH bend character. The anharmonic coupling of the OH bend results in a highly elongated OH bend excited-state absorption transition that indicates a large manifold of OH bend overtone/combination bands in the OH stretch region that leads to strong bend-stretch Fermi resonance interactions. The OH and OD stretch regions consist of broad ground-state bleach signals, but there is no clear evidence of ω21 excited-state absorptions due to rapid population relaxation arising from strong intramolecular coupling to bending, fingerprint, and low-frequency H-bond modes. Orientational relaxation dynamics persist for timescales longer than the vibrational lifetimes, with polarization anisotropy components decaying within approximately 2 and 10 periods of the O-O oscillation for the OH and OD stretch, respectively. The significant isotopic dependence of the orientational dynamics is discussed in the context of intramolecular mode coupling, diffusional processes, and contributions from proton/deuteron transfer dynamics.

Compactness regularization in the analysis of dipolar EPR spectroscopy data

Dipolar electron paramagnetic resonance (EPR) experiments, such as double electron–electron resonance (DEER), measure distributions of nanometer-scale distances between paramagnetic centers, which are valuable for structural characterization of proteins and other macromolecular systems. One challenge in the least-squares fitting analysis of dipolar EPR data is the separation of the inter-molecular contribution (background) and the intra-molecular contribution. For noisy experimental traces of insufficient length, this separation is not unique, leading to identifiability problems for the background model parameters and the long-distance region of the intra-molecular distance distribution. Here, we introduce a regularization approach that mitigates this by including an additional penalty term in the objective function that is proportional to the variance of the distance distribution and thereby penalizes non-compact distributions. We examine the reliability of this approach statistically on a large set of synthetic data and illustrate it with an experimental example. The results show that the introduction of compactness can improve identifiability.

Dipolar pathways in dipolar EPR spectroscopy.

Dipolar electron paramagnetic resonance (EPR) experiments such as double electron-electron resonance (DEER) measure distributions of nanometer-scale distances between unpaired electrons, which provide valuable information for structural characterization of proteins and other macromolecular systems. To determine these distributions from the experimental signal, it is critical to employ an accurate model of the signal. For dilute samples of doubly spin-labeled molecules, the signal is a product of an intramolecular and an intermolecular contribution. We present a general model based on dipolar pathways valid for dipolar EPR experiments with spin-1/2 labels. Our results show that the intramolecular contribution consists of a sum and the intermolecular contribution consists of a product over individual dipolar pathway contributions. We examine several commonly used dipolar EPR experiments in terms of dipolar pathways and show experimental results confirming the theoretical predictions. This multi-pathway model makes it possible to analyze a wide range of dipolar EPR experiments within a single theoretical framework.

Water as a Lévy Rotor.

A probability density function describing the angular evolution of a fixed-length atom-atom vector as a Lévy rotor is derived containing just two dynamical parameters: the Lévy parameter α and a rotational time constant τ. A Lévy parameter α<2 signals anomalous (non-Brownian) motion. Molecular dynamics simulation of water at 298K validates the probability density function for the intramolecular ^{1}H─^{1}H dynamics. The rotational dynamics of water is found to be approximately Brownian at subpicosecond time intervals, becomes increasingly anomalous at longer time intervals due to hydrogen-bond breaking and reforming, before becoming indistinguishable from Brownian dynamics beyond about 25ps. The Lévy rotor model is used to estimate the intramolecular contribution to the longitudinal nuclear-magnetic-resonance (NMR) relaxation rate R_{1,intra}. It is found that R_{1,intra} contributes 65%±7% to the overall relaxation rate of water at room temperature.

Aggregation‐induced emission of copper nanoclusters

AbstractCopper nanoclusters (Cu NCs) have recently emerged as promising luminophores, featuring ultra‐small size, reasonable photostability, large Stokes shift, and long emission lifetimes. Aggregation‐induced emission (AIE) has been often used to further improve both the emission intensity and stability of these clusters, with plenty of potential applications in the fields of chemical sensing and bioimaging. This review starts with a summary of the current understanding of emission mechanisms of Cu NCs and proceeds with the analysis of contributions from the Cu metal core and the organic ligands. We summarize the recent research progress on the design of ligands, and the ways on how to induce aggregation of the Cu NCs through electrostatic charge neutralization, host‐guest interactions, and the use of templates. We also discuss the current understanding of emission mechanisms of Cu NCs experiencing AIE, such as the often‐cited restriction of intramolecular motion and contributions from Cu(I) molecular complexes. We finish this review by providing concluding remarks and offering our own perspective on the active field of AIE of Cu NCs, with a hope to further promote the research on the fundamental aspects of this useful phenomenon.

Deconvolving Contributions to Decoherence in Molecular Electron Spin Qubits: A Dynamic Ligand Field Approach.

In the past decade, transition metal complexes have gained momentum as electron spin-based quantum bit (qubit) candidates due to their synthetic tunability and long achievable coherence times. The decoherence of magnetic quantum states imposes a limit on the use of these qubits for quantum information technologies, such as quantum computing, sensing, and communication. With rapid recent development in the field of molecular quantum information science, a variety of chemical design principles for prolonging coherence in molecular transition metal qubits have been proposed. Here the spin-spin, motional, and spin-phonon regimes of decoherence are delineated, outlining design principles for each. It is shown how dynamic ligand field models can provide insights into the intramolecular vibrational contributions in the spin-phonon decoherence regime. This minireview aims to inform the development of molecular quantum technologies tailored for different environments and conditions.

Rotational correlation times, diffusion coefficients and quadrupolar peaks of the protic ionic liquid ethylammonium nitrate by means of 1H fast field cycling NMR relaxometry

The protic ionic liquid (PIL) ethylammonium nitrate (EAN) is characterized by hydrogen bonding between the NH bonds of the cations and the oxygen atoms of the anions. The three-dimensional H-bond network of EAN very much resembles that of water. Although this first ionic liquid is known for more than 100 years, there is still lack of information about the rotational and translational dynamics, and how both are related to each other. For that purpose, we measured the 1H nuclear magnetic relaxation dispersion curves (NMRD) of EAN by means of Fast Field Cycling (FFC) NMR relaxometry. We were able to analyze the measured 1H spin-lattice relaxation rates R1 covering a large temperature range between 248 and 333 K simultaneously. Applying the well-known Bloembergen-Purcell-Pound (BPP) approach, we decomposed the total relaxation rates into intramolecular and intermolecular contributions, describing the rotational and translational dynamics of the ethylammonium cation. Here, we report rotational correlation times, τR, and translational diffusion coefficients, DT, both derived from the total 1H spin-lattice relaxation rates as a function of temperature and frequency. Self-diffusion coefficients, DT, were also determined from the total relaxation rates in the low frequency range, wherein only the intermolecular relaxation contribution is frequency dependent. Then, DT results from the slope of a linear fit of the spin-lattice relaxation rate R1 as a function of the square root of frequency, ν. The diffusion coefficients obtained from both methods are in good agreement with self-diffusion coefficients measured by pulsed-field-gradient (PFG) NMR. The rotational correlation times, τR, derived from the intramolecular 1H relaxation contribution were compared to correlation times obtained from high-field NMR deuteron relaxation experiments, dielectric spectroscopy (DS) and femto-second-infrared (fs-IR) spectroscopy. For EAN, we also observed a local enhancement of the 1H spin-lattice relaxation rates R1 at high frequencies. This so-called quadrupole relaxation enhancement (QRE) results from the interference of the Zeeman transition energy of the 1H spins and the energy difference of two levels of the quadrupole 14N nuclei. QRE is usually known for solids, but rarely for the liquid state as observed here for EAN. Overall, we show that FFC relaxometry provides access to rotational correlation times, translational diffusion coefficients and quadrupole relaxation enhancement at the same time.

Insights into the Spin-Lattice Dynamics of Organic Radicals Beyond Molecular Tumbling: A Combined Molecular Dynamics and Machine-Learning Approach

The prediction of spin-lattice dynamics is a challenging computational and theoretical problem due to the complex interplay among atomic motion and spin interactions. Here, we employ machine-learning paradigms to generate a first-principles-accurate and computationally inexpensive model that predicts both conformational energy and spin Hamiltonian parameters of an organic radical as function of its molecular distortions. This model is applied to the study of the g tensor correlation function during molecular dynamics in solution and it is shown that it is possible to access the time dependence of the spin Hamiltonian parameters without making assumptions on the type of molecular motion or spin-lattice dynamics’ time-scales involved. We further use these approach to disentangle inter- and intra-molecular contributions to the g tensor correlation function and provide new insights into the nature of vibronic-coupling in organic semiconductors.

Field-dependent paramagnetic relaxation enhancement in solutions of Ni(II): What happens above the NMR proton frequency of 1 GHz?

An extended set of paramagnetic relaxation enhancement (PRE) data, up to the field of 32.9 Tesla, is reported for protons in an acidified aqueous solution of a Ni(II) salt in the presence and in the absence of added glycerol. For the 55% w/w glycerol sample, a distinct maximum in the PRE vs magnetic field curve is observed for the first time. The data are analysed using the Swedish slow-motion theory, including both the intramolecular (inner-sphere) and intermolecular (outer-sphere) contributions. The results indicate that estimating the outer-sphere part in the presence of the more efficient inner-sphere term is a difficult task.

Reactivity of α,ω-Dihydrofluoropolyethers toward OH Predicted by Multiconformer Transition State Theory and the Interacting Quantum Atoms Approach.

We report rate constants for the tropospheric reaction between the OH radical and α,ω-dihydrofluoropolyethers, which represent a specific class of the hydrofluoropolyethers family with the formula HF2C(OCF2CF2)p(OCF2)qOCF2H. Four cases were considered: p0q2, p0q3, p1q0, and p1q1 (pxqy denoting p = x and q = y) with the calculations performed by a cost-effective protocol developed for bimolecular hydrogen-abstraction reactions. This protocol is based on multiconformer transition state theory and relies on computationally accessible M08-HX/apcseg-2//M08-HX/pcseg-1 calculations. Within the protocol's approximations, the results show that (1) the calculated rate constants are within a factor of five of the experimental results (p1q0 and p1q1) and (2) the chain length and composition have a negligible effect on the rate constants, which is consistent with the experimental work. The interacting quantum atoms energy decomposition scheme is used to analyze the observed trends and extract chemical information related to the imaginary frequencies and barrier heights that are key parameters controlling the reactivity of the reaction. The intramolecular exchange-correlation contributions in the reactants and transition states were found to be the dominating factor.

Thermal Conductivity via Entropy Scaling: An Approach That Captures the Effect of Intramolecular Degrees of Freedom

The thermal conductivity of gases depends strongly on the vibrational and rotational degrees of freedom of the molecule under consideration. Entropy scaling is based on the residual entropy, which does not capture the intramolecular and rotational contributions. This study proposes a model for the thermal conductivity that accounts for these degrees of freedom. We use the Chapman–Cowling approximation, where contributions of internal degrees of freedom to the thermal conductivity of an ideal gas are related to the self-diffusion coefficient. A resulting expression for the thermal conductivity is used as a reference in entropy scaling. We find experimental values for thermal conductivities in the entire fluid range to be (to good approximation) a function of residual entropy only. This study shows that entropy scaling is a strong approximation also for thermal conductivity, provided a suitable expression is chosen for the reference thermal conductivity.

Importance of zero-point energy for crystalline ice phases: A comparison of force fields and density functional theory.

Density functional theory (DFT) including van der Waals (vdW) interactions and accounting for zero-point energy (ZPE) is believed to provide a good description of crystalline ice phases [B. Pamuk et al., Phys. Rev. Lett. 108, 193003 (2012)]. Given the computational cost of DFT, it is not surprising that extensive phonon calculations, which yield the ZPE, have only been done for a limited amount of ice structures. Computationally convenient force fields on the other hand are the method of choice for large systems and/or dynamical simulations, e.g., of supercooled water. Here, we present a systematic comparison for seven hydrogen-ordered crystalline ice phases (Ih, IX, II, XIII, XIV, XV, and VIII) between many commonly used nonpolarizable force fields and density functionals, including some recently developed meta-GGA functionals and accounting for vdW interactions. Starting from the experimentally determined crystal structures, we perform space-group-constrained structural relaxations. These provide the starting point for highly accurate phonon calculations that yield effectively volume-dependent ZPEs within the quasiharmonic approximation. In particular, when including ZPE, the force fields show a remarkably good performance for equilibrium volumes and cohesive energies superior to many density functionals. A decomposition of the cohesive energies into intramolecular deformation, electrostatic, and vdW contributions quantifies the differences between force fields and DFT. Results for the equilibrium volumes and phase transition pressures for all studied force fields are much more strongly affected by ZPE than all studied density functionals. We track this down to significantly smaller shifts of the O-H-stretch modes and compare with experimental data from Raman spectroscopy.