Efficient exploration of reactive potential energy surfaces using Car-Parrinello molecular dynamics

Revealing the photochemical pathways of nitrate in water through first-principles simulations

The nitrate anion (NO3-) is abundant in environmental aqueous phases, including aerosols, surface waters, and snow, where its photolysis releases nitrogen oxides back into the atmosphere. Nitrate photolysis occurs via two channels: (1) the formation of NO2 and O- and (2) the formation of NO2- and O(3P). The occurrence of two reaction channels with very low quantum yield (∼1%) highlights the critical role of the solvation environment and spin-forbidden electronic transitions, which remain unexplained at the molecular level. We investigate the two photolysis channels in water using quantum chemical calculations and first-principles molecular dynamics simulations with hybrid density functional theory and enhanced sampling. We find that spin-forbidden absorption to the triplet state (T1) is possible but occurs at a rate ∼15 times weaker than the spin-allowed transition to the singlet state (S1). A metastable solvation cage complex requires additional thermal energy to dissociate the N-O bond, allowing for recombination or non-radiative deactivation. Our results explain the temperature dependence of photolysis, linked to hydrogen bond rearrangement in the solvation shell. This work provides new molecular insights into nitrate photolysis and its low quantum yield under environmental conditions.

Computational framework for discovery of degradation mechanisms of organic flow battery electrolytes

The stability of organic redox-active molecules is a key challenge for the long-term viability of organic redox flow batteries (ORFBs). Electrolyte degradation leads to capacity fade, reducing the efficiency and lifespan of ORFBs. To systematically investigate degradation mechanisms, we present a computational framework that automates the exploration of degradation pathways. The approach integrates local reactivity descriptors to generate reactive complexes and employs a single-ended process search to discover elementary reaction steps, including transition states and intermediates. The resulting reaction network is iteratively refined with heuristics and human-guided validation. The framework is applied to study the degradation mechanisms of quinone- and quinoxaline-based electrolytes under acidic and basic aqueous conditions. The predicted reaction pathways and degradation products align with experimental observations, highlighting key degradation modes such as Michael addition, disproportionation, dimerization, and electrochemical transformation. The framework provides a valuable tool for in silico screening of stable electrolyte candidates and guiding the molecular design of next-generation ORFBs.

Oxysterols Modulate Protein-Sterol Interactions to Impair CXCR4 Signaling in Aging Cells

Organismal aging is accompanied by the accumulation of senescent cells in the body, which drives tissue dysfunction. Senescent cells have a distinctive profile, including proliferation arrest, resistance to apoptosis, altered gene expression, and high inflammation. Despite global signaling and metabolic dysregulation during senescence, the underlying reasons for changes in signaling remain unclear. GPCRs are pivotal in cellular signaling, dynamically mediating the complex interplay between cells and their surrounding environment to maintain cellular homeostasis. The chemokine receptor CXCR4 plays a crucial role in modulating immune responses and inflammation. It has been shown that the expression of CXCR4 increases in cells undergoing senescence, which enhances inflammation postactivation. Here, we examine CXCR4 signaling in deeply senescent cells (aged cells), where cholesterol and its oxidized derivatives, oxysterols, affect receptor function. We report elevated oxysterol levels in senescent cells, which altered classical CXCL12-mediated CXCR4 signaling. Tail-oxidized sterols disrupted signaling more than ring-oxidized counterparts. Molecular dynamics simulations revealed that 27-hydroxycholesterol displaces cholesterol and binds strongly to alter the conformation of critical signaling residues, modifying the sterol-CXCR4 interaction landscape. Our study provides a molecular view of the observed mitigated GPCR signaling in the presence of oxysterols, which switched G-protein signaling from Gαi/o to Gαs class. Overall, we present an altered paradigm of GPCR signaling, where cholesterol oxidation alters the signaling outcome in aged cells.

Theoretical Study of the Reaction of Hydrogen Selenide with the Cl• Atom and the •OH Radical, and Differences with the Behavior of Other Hydrogen Chalcogenides

Hydrogen selenide, H2Se, is the third-row analog of hydrogen sulfide, H2S, and water, H2O. While there is ample thermochemical and kinetic information about the reactions of the latter two species, few experimental or theoretical data are available on H2Se. In this work, we use high-level post-Hartree-Fock methods to study the reaction of H2Se with two of the most abundant atmospheric radical species, the Cl• atom and the •OH radical, H2Se + Cl• → HSe• + HCl H2Se + •OH → HSe• + H2O We used the SVECV-f12 composite quantum chemical method to study the stability of adducts and transition states, as well as the barriers for the transformations. It was found that a correct representation of the barrierless adduct is crucial for a correct description of the reaction's kinetics, and we present in this paper the first theoretical determination of the reaction coefficient of H2Se with Cl• in the literature, obtaining a value of 5.7 × 10-10 cm3 molecule-1 s-1, in excellent agreement with the experimental determination of 5.5 × 10-10 cm3 molecule-1 s-1 at room temperature Additionally, using the same procedure, we obtained a value of 6.4 × 10-11 cm3 molecule-1 s-1 for the reaction with •OH, in this case slightly smaller than the only previous estimation of 7.2 × 10-11 cm3 molecule-1 s-1 obtained indirectly from similar reactions for sulfur compounds, in all cases at 298.15 K. Judging from the agreement of the theoretical and experimental rate coefficients in the case of the reaction with chlorine, we suggest that our value for the reaction with the hydroxyl radical is more accurate than the estimated one. A comparison of the dependence of the rate coefficients for H2S and H2Se as a function of the temperature shows some noticeable differences. A convex behavior of the T-dependence for the Cl• reaction at high temperatures was found, instead of the concave behavior found for sulfur. Nevertheless, this is not important in atmospheric chemistry conditions, and a sufficiently linear region was found with the expression, k(Cl•) = 1.6 × 10-10 exp (0.7/RT) cm3 molecule-1 s-1. The reaction with •OH is even more complicated, with nonlinear tail at high (combustion) and low (stratosphere) temperatures, while the region important in tropospheric chemistry could be fitted with the Arrhenius equation k(•OH) = 5.9 × 10-12 exp (1.4/RT) cm3 molecule-1 s-1. Using our theoretically determined kinetic data, we were also able to calculate the atmospheric lifetime of H2Se as 2.6 h, considerably shorter than that of H2S (12.2 h).

Striking Impact of Solvent Polarity on the Strength of Hydrogen-Bonded Complexes: A Nexus Between Theory and Experiment

The binding free energy of hydrogen-bonded complexes is generally inversely proportional to the solvent dielectric constant. This occurs because the solvent-accessible surface area of the complex is always smaller than that of the individual subsystems, leading to a reduction in solvation energy. The present study explores the potential for stabilizing hydrogen-bonded complexes in a solvent with higher polarity. Contrary to the established understanding, we have demonstrated that the hydrogen-bonded complex (CH3CH2COOH⋅⋅⋅2,4,6-trimethylpyridine) can be better stabilized in a solvent with higher polarity. In this case, a significant charge transfer between the subsystems results in an increased dipole moment of the complex, leading to its stabilization in a more polar solvent. The expected inverse relationship between binding free energy and solvent dielectric constant is observed when the charge transfer between the subsystems is low. Thus, the magnitude of the charge transfer between subsystems is possibly the key factor in determining the stabilization or destabilization of H-bonded complexes in different solvents. Here, we present a comprehensive study that combines experimental and theoretical approaches, including nuclear magnetic resonance (NMR), infrared (IR) spectroscopies and quantum chemical calculations to validate the findings.

Mechanistic Insight on Ethanol Driven Swelling and Disruption of Cholesterol Containing Biomimetic Vesicles From Coarse-Grained Molecular Dynamics

We have performed coarse-grained (CG) molecular dynamics (MD) simulations to delineate the impact of ethanol (EtOH) on cholesterol (CHOL) containing biomimetic bilayer and vesicle composed of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipids. We have first deduced the missing interaction parameters for the POPC-CHOL-EtOH-water system within the SPICA/SDK CG force-field (CG-FF). By monitoring the electron density profiles, the orientational order parameter, and reproducing the all-atom MD-derived free energy for the insertion of ethanol from the bulk aqueous phase to the hydrophobic core of the POPC-CHOL lipid bilayer, we successfully determined all the missing non-bonding interaction parameters for the POPC-CHOL-EtOH-water system. The proposed force field was applied to investigate the effect of ethanol at various concentrations on unilamellar vesicles composed of POPC and cholesterol. It was found that 40 mol% or more concentration of ethanol is required to disintegrate or rupture the POPC-CHOL vesicle membranes. While cholesterol offers some resilience against the detrimental effects of ethanol, we still observe an increase in vesicle size (swelling) and a contraction in the bilayer thickness (thinning) as ethanol concentration rises from 0 to 30 mol%. At ethanol concentrations exceeding 30 mol%, the vesicles become increasingly susceptible to disintegration due to enhanced penetration of ethanol and water molecules into the hydrophobic core of the membranes.

High-Performance Proton Exchange Membrane with Vertically Aligned Montmorillonite Nanochannels

The traditional perfluorosulfonic acid proton exchange membrane is crucial for proton exchange membrane fuel cells, but its high cost has impeded broader commercialization. In this study, a novel concept of a cost-effective and stable vertically aligned polydopamine-intercalated montmorillonite membrane (VAPMM) is introduced. 2D nanochannels formed within the lamellar structure of polydopamine-coated montmorillonite nanosheets provide a significant stable in-plane proton conductivity of 0.58 S cm-1. The stacked lamellar structure is embedded in epoxy resin to maintain its orientation. Subsequently, precise slicing along the vertical direction of the 2D nanochannels yields a thin film ≈150 µm thick, featuring vertically aligned proton conductive transmembrane nanochannels. When assembled into a membrane electrode assembly with commercial gas diffusion electrodes, the VAPMM exhibits a maximum areal peak power density of up to 534.00 mW cm-2 at 75 °C with 100% RH, surpassing by more than four times that of a commercial Nafion membrane of similar thickness (N117, 183 µm, 116.17 mW cm-2). This study outlines a pathway for developing next-generation proton exchange membranes that are both cost-effective and highly stable. Additionally, it introduces a straightforward method to create fully vertically aligned transmembrane nanochannels while preserving the interlayer structure, which is crucial for advancements in nanofluidics.

Discrete state model of a self-aggregating colloidal system with directional interactions

The construction of coarse-grained descriptions of a system's kinetics is well established in biophysics. One prominent example is Markov state models in protein folding dynamics. In this paper, we develop a coarse-grained, discrete state model of a self-aggregating colloidal particle system inspired by the concepts of Markov state modeling. The specific self-aggregating system studied here involves field-responsive colloidal particles in orthogonal electric and magnetic fields. Starting from particle-resolved (Brownian dynamics) simulations, we define the discrete states by categorizing each particle according to its local structure. We then describe the kinetics between these states as a series of stochastic, memoryless jumps. In contrast to other works on colloidal self-assembly, our coarse-grained approach describes the simultaneous formation and evolution of multiple aggregates from single particles. Our discrete model also takes into account the changes in transition dynamics between the discrete states as the size of the largest cluster grows. We validate the coarse-grained model by comparing the predicted population fraction in each of the discrete states with those calculated directly from the particle-resolved simulations as a function of the largest cluster size. We then predict population fractions in the presence of noise-averaging and in a situation where a model parameter is changed instantaneously after a certain time. Finally, we explore the validity of the detailed balance condition in the various stages of aggregation.

Elucidating and contrasting the mechanisms for Mg and Ca sulfate ion-pair formation with multi-level embedded quantum mechanics/molecular dynamics simulations

Solutions and minerals containing sulfate (SO42-), and Ca2+ and Mg2+ cations, are ubiquitous throughout the lithosphere and are significant components of seawater, thus presenting a prototypical system for the study of strong electrolytes and crystal nucleation mechanisms. However, despite their relative abundance, key questions remain unanswered about the most fundamental atomic-level steps of their mineralization pathways and aqueous dynamics. Here, we carry out enhanced sampling multi-level molecular dynamics (MD) embedded correlated wavefunction theory simulations to elucidate ion-pairing mechanisms for Mg-SO4 and Ca-SO4 in concentrated aqueous solution, accurately capturing effects arising from both structural dynamics and electron exchange-correlation. We predict contact-ion-pair formation to be barrierless and highly exoergic for Ca-SO4, in agreement with its minimal solubility, whereas for Mg-SO4, solvent-shared and contact ion pairs have similar free energies, qualitatively consistent with its higher solubility. Finally, we demonstrate that brief high-temperature pre-equilibration may be utilized to accelerate convergence of free energies in blue-moon-ensemble enhanced-sampling MD.

An Atomic-Scale Explanation for The High Selectivity Towards Carbon Dioxide Reduction Observed On Liquid Metal Catalysts

The low-temperature liquid metals Ga-In and Ga-Sn have previously showcased >95 % selectivity towards the electrochemical reduction of CO2 to formate, occuring only when the alloys are melted, not solid. Here, density functional theory molecular dynamics and metadynamics simulations reveal that CO2 does not directly adsorb to the Ga-alloy surface, but instead is reduced indirectly by reaction with an adsorbed hydrogen. The reaction barrier is vastly more favourable when this process occurs at In or Sn sites (average: 0.26 eV), than when it occurs on Ga (average: 0.47 eV). However, there is no difference in barrier between solid and liquid surfaces. Instead, we find that Hads is mobile only on the liquid surface, travelling due to the motion of the liquid beneath. This process drives Hads to In/Sn sites, allowing low-barrier CO2 reduction to occur only on the liquid. Therefore, the dynamic motion of liquid metal catalysts can underpin their unique reactivity. The result has far reaching implications for any protonation reaction conducted with a liquid metal catalyst.

Second-Order Mass-Weighting Scheme for Atom-Centered Density Matrix Propagation Molecular Dynamics

The atom-centered density matrix propagation (ADMP) method is an extended Lagrangian approach to ab initio molecular dynamics, which includes the density matrix in an orthonormalized atom-centered Gaussian basis as additional, fictitious, electronic degrees of freedom, classically propagated along with the nuclear ones. A high adiabaticity between the nuclear and electronic subsystems is mandatory in order to keep the trajectory close to the Born-Oppenheimer (BO) surface. In this regard, the fictitious electronic mass μ, being a symmetric, nondiagonal matrix in its most general form, represents a free parameter, exploitable to optimize the propagation of the electronic density. Although mass-weighting schemes in ADMP exist, a systematic procedure to define an optimal value of the fictitious masses is not available yet. In this work, in order to rationally evaluate the electronic mass, fictitious electronic normal modes are defined through the diagonalization of the Hessian of the electronic density matrix. If the same frequency is imposed on all such modes (compatible with the chosen integration time step), then the corresponding μ matrix can be calculated and then employed for the following propagation. Analysis of several ADMP test simulations reveals that such Hessian-based mass-weighting approach is able to ensure, together with a 0.1/0.2 fs time steps, a high separation between the (real) nuclear and the (fictitious) electronic frequencies, which determines a high adiabaticity. This high, unprecedented, accuracy in the propagation leads, in turn, to low errors in the estimated nuclear vibrational frequencies, making the ADMP method totally comparable to a fully converged BO molecular dynamics simulation but more computationally efficient. This work, therefore, contributes to a further development of the ADMP ab initio molecular dynamics method, aimed at improving its accuracy through a more rational evaluation of the fictitious electronic mass parameter.

Metadynamics investigation of lanthanide solvation free energy landscapes and insights into separations energetics

Lanthanide ion solvation chemistry in nonaqueous phases is key to understanding and developing effective separation processes for these critical materials. Due to the complexity and inherent disorder of the solution phase, a comprehensive picture of the solvated metal ion is often difficult to generate solely from conventional spectroscopic approaches and electronic structure calculations, particularly in the extractant phase. In this work, we use classical molecular dynamics (MD) simulation with an advanced sampling technique, metadynamics, supplemented by experimental spectroscopy and speciation analysis, to measure lanthanide solvation free energy landscapes. We define coordination-based collective variables to probe the entire range of solvation configurations in the organic phase of lanthanum (La), europium (Eu), and lutetium (Lu) nitrate salts bound with a commonly used extractant, N,N'-dimethyl, N,N'-dioctylhexylethoxymalonamide (DMDOHEMA). The known lanthanide extraction trend of La ≈ Eu > Lu is readily explained by the measured free energy surfaces, which show consistent DMDOHEMA coordination from La to Eu, followed by loss of DMDOHEMA coordination from Eu to Lu. These simulations suggest how ligand crowding at the metal center can control selectivity, in this case resulting in the opposite extraction trend as observed with other conventional extractants, where the enthalpic contribution from increasing lanthanide charge density across the series dominates the extraction energetics. We also find that the presence of inner-sphere water, verified by time-resolved fluorescence, diversifies the accessible solvation structures. As a result, understanding solvation requires consideration of an entire thermodynamic ensemble, rather than the single dominant lowest-energy structure, as is often considered out of necessity in interpretation of spectroscopic data or in electronic structure-based ligand design approaches. In general, we demonstrate how metadynamics uniquely enables investigation of complex, multidimensional solvation energetic landscapes, and how it can explain selectivity trends where extraction is controlled by more complex mechanisms than simple charge density-based selectivity.

Structures of Th4+ aqueous solutions: insights from AIMD and metadynamics simulations

Solution chemistry of actinide ions is critical to understanding the solvation behaviors and hydrolysis process. Using tetravalent thorium ion Th4+ as a representative example, we investigate the local structures and dynamic behaviors of hydrated Th4+ ions by ab initio molecular dynamics (AIMD) simulations using the recently developed norm-conserving pseudopotentials and basis sets optimized for actinides (J.-B. Lu et al., J. Chem. Theory Comput. 2021, 17, 3360-3371). AIMD simulations reveal two distinct solvation shells, with the first shell comprising 9 water molecules at approximately rTh-O = 2.50 Å and exhibiting a tricapped trigonal prism geometry. These conclusions are confirmed through metadynamics simulations and further structural analysis. AIMD simulations also show the slight effect of temperature and counterions on the structure of the solution. The structured solvation shells of the highly charged Th4+ ion with the specific geometry, distinct from the structure of liquid water, lead to corresponding structural changes in the hydrogen bond network in water. Additionally, beyond the solvent-shared ion pair (SIP) state observed in the unbiased AIMD simulations, the metadynamics simulations reconstruct a two-dimensional free energy surface that clearly indicates the potential stability of the contact ion pair (CIP) state in the system with Cl- as a counterion. The findings in this work provide insights into the solution chemistry of actinides and serve as a reference for studying other actinide solution systems.

Temperature-dependent Li-ion transport in lithium lanthanum titanate electrolytes

A shift of the Li+ ion hopping mechanism with temperature in solid-state lithium lanthanum titanate (LLTO) electrolytes was discovered using ab initio metadynamics simulations. The low-temperature potential-energy barriers were calculated for pristine, nitrogen-doped, vacancy-containing LLTO, revealing nitrogen dopants in the La-poor layer and oxygen vacancies as the key factors for enhanced ionic conductivity.

Computational Spectroscopy of Aqueous Solutions: The Underlying Role of Conformational Sampling

Fully atomistic multiscale polarizable quantum mechanics (QM)/molecular mechanics (MM) approaches, combined with techniques to sample the solute-solvent phase space, constitute the most accurate method to compute spectral signals in aqueous solution. Conventional sampling strategies, such as classical molecular dynamics (MD), may encounter drawbacks when the conformational space is particularly complex, and transition barriers between conformers are high. This can lead to inaccurate sampling, which can potentially impact the accuracy of spectral calculations. For this reason, in this work, we compare classical MD with enhanced sampling techniques, i.e., replica exchange MD and metadynamics. In particular, we show how the different sampling techniques affect computed UV, electronic circular dichroism, nuclear magnetic resonance shielding, and optical rotatory dispersion of N-acetylproline-amide in aqueous solution. Such a system is a model peptide characterized by complex conformational variability. Calculated values suggest that spectral properties are influenced by solute conformers, relative population, and solvent effects; therefore, particular care needs to be paid for when choosing the sampling technique.

Electrolyte Dependence of Li+ Transport Mechanisms in Small Molecule Solvents from Classical Molecular Dynamics

As demands on Li-ion battery performance increase, the need for electrolytes with high ionic conductivity and a high Li+ transference number (tLi) becomes crucial to boost power density. Unfortunately, tLi in liquid electrolytes is typically <0.5 due to Li+ migrating via a vehicular mechanism, whereby Li+ diffuses along with its solvation shell, making its diffusivity slower than the counteranion. Designing liquid electrolytes where the Li+ ion diffuses independently of its solvation shell is of significant interest to enhance the transference number. In this work, we elucidate how the properties of the solvent influence the Li+ transport mechanism. Using classical molecular dynamics simulations, we find that a vehicular mechanism can be increasingly preferred with a decreasing solvent viscosity and increasing interaction energy between the solvent and Li+. Thus, a weaker interaction energy can enhance tLi through a solvent-exchange mechanism, ultimately improving Li-ion battery performance. Finally, metadynamics simulations show that in electrolytes where a solvent-exchange mechanism is preferable, the energy barrier to changing the coordination environment of Li+ is much lower than in electrolytes where a vehicular mechanism dominates.

Dynamic dissolution of Cm3+ ions incorporated at the calcite-water interface: an ab initio molecular dynamics simulation study

The stability of actinide-mineral solid solution in a water environment is critical for assessing the safety of nuclear-waste geological repositories and studying actinide migration in natural systems. However, the dissolution behavior of actinide ions incorporated at the mineral-water interface is still unclear at the atomic level. Herein, we present metadynamics simulations of the reaction pathways, thermodynamics and kinetics of trivalent curium ions (Cm3+) dissolving from calcite surfaces. Cm3+ ions incorporated in different calcite surfaces (i.e., terrace and stepped surfaces) with distinct coordination environments have different reaction pathways, free energy barriers and free energy changes. We found that Cm dissolution from a stepped surface is more favorable than that from a terrace surface, both thermodynamically and kinetically. In addition, water molecules seem to promote the detachment of curium ions from the surface by exerting a pulling force via water coordination with Cm3+ and a pushing force via proton migration to the surface layer and water diffusion in the vacant Cm site. Thus, the findings from this work prove to be a milestone in revealing the dynamic dissolution mechanism of trivalent actinides from minerals and would also help predict the dissolution behaviors of other metal ions at the solid-water interface in chemical and environmental sciences.

A theoretical study of the mechanism of cationic polymerization of isobutylene catalysed by EtAlCl2/t-BuCl with bis(2-chloroethyl)ether in hexanes

The mechanism of cationic polymerization of isobutylene catalyzed by t-BuCl/ethylaluminum dichloride (EADC) combined with bis(2-chloroethyl)ether (CEE) in n-hexane solvent has been investigated using ab initio molecular dynamics (AIMD) and metadynamics (MTD) simulations. The results indicated that the polyisobutylene (PIB) initiation stage involves a clear two-step mechanism. Calculation of the free energy landscapes of the other two ether reactions reveals that the energy barriers of diisopropyl ether (i-Pr2O) and 2-chloroethyl ethyl ether (CEEE) are much higher than those of CEE, which is consistent with the experimental results. During the chain propagation phase, the required free energy barrier gradually decreases and tends to reach equilibrium as the chain length increases. Finally, the oxonium mechanism during the chain initiation stage was investigated by calculating the 1H NMR spectra and MTD simulation. Our calculations can confirm that the existence of tert-butyloxonium ions during the reaction is possible. Their contribution to the whole reaction is further discussed.

Stability of Cytoplasmic Membrane of Escherichia coli Bacteria in Aqueous and Ethanolic Environment

The mechanism of action of any antibacterial agent or disinfectant depends largely on their interaction with the bacterial membrane. Herein, we use the SPICA (surface property fitting coarse graining) force-field and develop a coarse-grained (CG) model for the structure of the cytoplasmic membrane of Escherichia coli (E. coli) and its interaction with water and ethanol. We elucidate the impact of different concentrations of ethanol on the cytoplasmic membrane bilayers and vesicles of E. coli using the CG molecular dynamics (CG MD) simulations. Our modeling approach first focuses on the parametrization of the required force-field for POPG lipid and its interaction with water, ethanol, and POPE lipid. Subsequently, the structural stability of the E. coli bacterial membrane in the presence of high and low concentrations of ethanol is delineated. Both flat bilayers as well as vesicles of E. coli membrane were considered for the CG MD. Our results reveal that, at low ethanol concentrations (<30 mol %), the size of the E. coli vesicles increases with discernible deformations in their shapes. Because of ethanol-induced interdigitation, thinning of the E. coli vesicular membrane is also observed. However, at higher ethanol concentrations (>30 mol %), the integrity of the vesicles is lost because of deteriorating invasion of ethanol molecules into the vesicle bilayer and significant weakening of lipid-lipid interactions. At higher ethanol concentrations (40 and 70 mol %), both the multivesicle and single-vesicle bacterial membranes exhibit a similar rupturing pattern wherein the extraction of lipids from the membrane and formation of aggregates of the component lipids are observed. These aggregates consist of polar head groups of 3-5 POPE/POPG lipids with intertwined nonpolar tails.

What to Make of Zero: Resolving the Statistical Noise from Conformational Reorganization in Alchemical Binding Free Energy Estimates with Metadynamics Sampling

We introduce the self-relative binding free energy (self-RBFE) approach to evaluate the intrinsic statistical variance of dual-topology alchemical binding free energy estimators. The self-RBFE is the relative binding free energy between a ligand and a copy of the same ligand, and its true value is zero. Nevertheless, because the two copies of the ligand move independently, the self-RBFE value produced by a finite-length simulation fluctuates and can be used to measure the variance of the model. The results of this validation provide evidence that a significant fraction of the errors observed in benchmark studies reflect the statistical fluctuations of unconverged estimates rather than the models' accuracy. Furthermore, we find that ligand reorganization is a significant contributing factor to the statistical variance of binding free energy estimates and that metadynamics-accelerated conformational sampling of the torsional degrees of freedom of the ligand can drastically reduce the time to convergence.

Electron-beam-promoted fullerene dimerization in nanotubes: insights from DFT computations

Fullerene dimerization inside a peapod is analyzed at DFT level by characterizing the stationary points and deriving the energy profile of the initial and reversible process named phase 1. We find that the barriers for the radical cation mechanism are significantly lower than those found for the neutral pathway. The peapod is mainly providing one-dimensional confinement for the reaction to take place in a more efficient way. Car-Parrinello metadynamics simulations provide hints on structures for the initial steps of the irreversible phase 2 where bond formation and breaking lead to important structural reorganizations within the coalescence process.

A Rigorous Framework for Calculating Protein-Protein Binding Affinities in Membranes

Calculating the binding free energy of integral transmembrane (TM) proteins is crucial for understanding the mechanisms by which they recognize one another and reversibly associate. The glycophorin A (GpA) homodimer, composed of two α-helical segments, has long served as a model system for studying TM protein reversible association. The present work establishes a methodological framework for calculating the binding affinity of the GpA homodimer in the heterogeneous environment of a membrane. Our investigation carefully considered a variety of protocols, including the appropriate choice of the force field, rigorous standardization reflecting the experimental conditions, sampling algorithm, anisotropic environment, and collective variables, to accurately describe GpA dimerization via molecular dynamics-based approaches. Specifically, two strategies were explored: (i) an unrestrained potential mean force (PMF) calculation, which merely enhances sampling along the separation of the two binding partners without any restraint, and (ii) a so-called "geometrical route", whereby the α-helices are progressively separated with imposed restraints on their orientational, positional, and conformational degrees of freedom to accelerate convergence. Our simulations reveal that the simplified, unrestrained PMF approach is inadequate for the description of GpA dimerization. Instead, the geometrical route, tailored specifically to GpA in a membrane environment, yields excellent agreement with experimental data within a reasonable computational time. A dimerization free energy of -10.7 kcal/mol is obtained, in fairly good agreement with available experimental data. The geometrical route further helps elucidate how environmental forces drive association before helical interactions stabilize it. Our simulations also brought to light a distinct, long-lived spatial arrangement that potentially serves as an intermediate state during dimer formation. The methodological advances in the generalized geometrical route provide a powerful tool for accurate and efficient binding-affinity calculations of intricate TM protein complexes in inhomogeneous environments.

An integrative approach unveils a distal encounter site for rPTPε and phospho-Src complex formation

The structure determination of protein tyrosine phosphatase (PTP): phospho-protein complexes, which is essential to understand how specificity is achieved at the amino acid level, remains a significant challenge for protein crystallography and cryoEM due to the transient nature of binding interactions. Using rPTPεD1 and phospho-SrcKD as a model system, we have established an integrative workflow to address this problem, by means of which we generate a protein:phospho-protein complex model using predetermined protein structures, SAXS and pTyr-tailored MD simulations. Our model reveals transient protein-protein interactions between rPTPεD1 and phospho-SrcKD and is supported by three independent experimental validations. Measurements of the association rate between rPTPεD1 and phospho-SrcKD showed that mutations on the rPTPεD1: SrcKD complex interface disrupts these transient interactions, resulting in a reduction in protein-protein association rate and, eventually, phosphatase activity. This integrative approach is applicable to other PTP: phospho-protein complexes and the characterization of transient protein-protein interface interactions.

Automated Exploration of Reaction Networks and Mechanisms Based on Metadynamics Nanoreactor Simulations

We developed an automated approach to construct a complex reaction network and explore the reaction mechanisms for numerous reactant molecules by integrating several theoretical approaches. Nanoreactor-type molecular dynamics was used to generate possible chemical reactions, in which the metadynamics was used to overcome the reaction barriers, and the semiempirical GFN2-xTB method was used to reduce the computational cost. Reaction events were identified from trajectories using the hidden Markov model based on the evolution of the molecular connectivity. This provided the starting points for further transition-state searches at the electronic structure levels of density functional theory to obtain the reaction mechanism. Finally, the entire reaction network containing multiple pathways was built. The feasibility and efficiency of the automated construction of the reaction network were investigated using the HCHO and NH3 biomolecular reaction and the reaction network for a multispecies system comprising dozens of HCN and H2O molecules. The results indicated that the proposed approach provides a valuable and effective tool for the automated exploration of the reaction networks.

Modern Alchemical Free Energy Methods for Drug Discovery Explained

This Perspective provides a contextual explanation of the current state-of-the-art alchemical free energy methods and their role in drug discovery as well as highlights select emerging technologies. The narrative attempts to answer basic questions about what goes on "under the hood" in free energy simulations and provide general guidelines for how to run simulations and analyze the results. It is the hope that this work will provide a valuable introduction to students and scientists in the field.

Solvent-Induced Symmetry Breaking of the Photoinduced Charge Transfer Dynamics in the Bridged Perylene Dimer

The charge transfer dynamics of the bridged perylene dimer were investigated with the recently developed solvent coupling Redfield time propagation model. The results are compared with previous experimental findings to showcase the significance and applicability of the model. The charge transfer dynamics in vacuum showed that no breaking of the charge transfer direction symmetry occurred upon optical excitation, in perfect agreement with the experiment. Meanwhile, attractive solute-solvent interactions facilitated by the dipole moments of the polar solvents were observed to break the charge transfer direction symmetry. The conformational isomerism effect on the transfer dynamics manifested itself by promoting different transport channels upon solvation. Consequently, the solvent coupling Redfield time propagation model was indeed found to be able to quantitatively describe the charge transfer dynamics including exotic phenomena such as symmetry breaking of charge transfer direction.

An interoperable implementation of collective-variable based enhanced sampling methods in extended phase space within the OpenMM package

Collective variable (CV)-based enhanced sampling techniques are widely used today for accelerating barrier-crossing events in molecular simulations. A class of these methods, which includes temperature accelerated molecular dynamics (TAMD)/driven-adiabatic free energy dynamics (d-AFED), unified free energy dynamics (UFED), and temperature accelerated sliced sampling (TASS), uses an extended variable formalism to achieve quick exploration of conformational space. These techniques are powerful, as they enhance the sampling of a large number of CVs simultaneously compared to other techniques. Extended variables are kept at a much higher temperature than the physical temperature by ensuring adiabatic separation between the extended and physical subsystems and employing rigorous thermostatting. In this work, we present a computational platform to perform extended phase space enhanced sampling simulations using the open-source molecular dynamics engine OpenMM. The implementation allows users to have interoperability of sampling techniques, as well as employ state-of-the-art thermostats and multiple time-stepping. This work also presents protocols for determining the critical parameters and procedures for reconstructing high-dimensional free energy surfaces. As a demonstration, we present simulation results on the high dimensional conformational landscapes of the alanine tripeptide in vacuo, tetra-N-methylglycine (tetra-sarcosine) peptoid in implicit solvent, and the Trp-cage mini protein in explicit water.

DFT-assisted low-dimensional carbon-based electrocatalysts design and mechanism study: a review

Low-dimensional carbon-based (LDC) materials have attracted extensive research attention in electrocatalysis because of their unique advantages such as structural diversity, low cost, and chemical tolerance. They have been widely used in a broad range of electrochemical reactions to relieve environmental pollution and energy crisis. Typical examples include hydrogen evolution reaction (HER), oxygen evolution reaction (OER), oxygen reduction reaction (ORR), carbon dioxide reduction reaction (CO2RR), and nitrogen reduction reaction (NRR). Traditional "trial and error" strategies greatly slowed down the rational design of electrocatalysts for these important applications. Recent studies show that the combination of density functional theory (DFT) calculations and experimental research is capable of accurately predicting the structures of electrocatalysts, thus revealing the catalytic mechanisms. Herein, current well-recognized collaboration methods of theory and practice are reviewed. The commonly used calculation methods and the basic functionals are briefly summarized. Special attention is paid to descriptors that are widely accepted as a bridge linking the structure and activity and the breakthroughs for high-volume accurate prediction of electrocatalysts. Importantly, correlated multiple descriptors are used to systematically describe the complicated interfacial electrocatalytic processes of LDC catalysts. Furthermore, machine learning and high-throughput simulations are crucial in assisting the discovery of new multiple descriptors and reaction mechanisms. This review will guide the further development of LDC electrocatalysts for extended applications from the aspect of DFT computations.

In silico Investigation of the Thermochemistry and Photoactivity of Pyruvic Acid in an Aqueous Solution of NaCl

The photochemistry of oxocarboxylic acids contributes significantly to the complex chemistry occurring in the atmosphere. In this regard, pyruvic acid undergoes photoreactions that lead to many diverse products. The presence of sodium cation near pyruvic acid in an aqueous solution, or its conjugate base in non-acidic conditions, influences the hydration equilibrium and the photosensitivity to UV-visible light of the oxocarboxylic acid. We performed an ab initio metadynamics simulation which serves two purposes: first, it unveils the mechanisms of the reversible hydration reaction between the keto and the diol forms, with a free-energy difference of only 2 kJ/mol at 300 K, which shows the influence of sodium on the keto/diol ratio; second, it provides solvent-shared ion pairing (SSIP) and contact ion pairing (CIP) structures, including Na+ coordinated to carbonyl, for the calculations of the electronic transition energies to an antibonding π* orbital, which sheds light on the photoactivity of these two forms in the actinic region.

Free Energy Landscapes of the Tautomeric Interconversion of Pyridoxal 5'-Phosphate Aldimines at the Active Site of Ornithine Decarboxylase in Aqueous Media

The pyridoxal 5'-phosphate (PLP) acts as a coenzyme for a large number of biochemical reactions. It exists in mainly two bound forms at the active site of the concerned enzyme: the internal aldimine, in which the PLP is bound with the ϵ-amino group of lysine at the active site, and the external aldimine, where the PLP is bound to the substrate amino acid. Both the internal and external aldimines have Schiff base linkage (N-H-O) and can exist in two tautomeric structures of ketoenamine and enolimine forms. In this work, we have investigated the free energy landscape for the tautomeric proton transfer in the internal and external aldimines at the active site of the ornithine decarboxylase enzyme in an aqueous medium. We performed hybrid quantum-classical metadynamics and force field-based molecular dynamics simulations, which revealed that the ketoenamine tautomer is more stable than the enolimine form. The QM/MM metadynamics calculations show that the free energy difference between the ketoenamine and enolimine forms for the internal aldimine is 3.9 kcal/mol, and it is found to be 5.8 kcal/mol for the external aldimine, with the ketoenamine form being more stable in both cases. The results are further supported by calculations of the binding free energies from classical simulations and static quantum chemical calculations in different environments. We have also analyzed the configurational structure of the microenvironment at the active site in order to have better insights into the interactions of the active site residues with the PLP in its two tautomeric forms.

Conformational flexibility of the disaccharide β-L-Fucp-(1→4)-α-D-Glcp-OMe as deduced from NMR spectroscopy experiments and computer simulations

Carbohydrates in biological systems are referred to as glycans and modification of their structures is a hallmark indicator of disease. Analysis of the three-dimensional structure forms the basis for further insight into how they function and comparison of crystal structure with solution-state conformation(s) is particularly relevant, which has been performed for the disaccharide β-L-Fucp-(1→4)-α-D-Glcp-OMe. In water solution the conformational space at the glycosidic linkage between the two sugar residues is identified from molecular dynamics (MD) simulations as having a low-energy exo-syn conformation, deviating somewhat from the solid-state conformation, and two anti-conformational states, i.e., anti-ϕ and anti-ψ, indicating flexibility at the glycosidic linkage. NMR data were obtained from 1D 1H,1H-NOESY and STEP-NOESY experiments, measurement of transglycosidic 3JCH coupling constants and NMR spin-simulation. The free energy profile of the ω torsion angle computed from MD simulation was in excellent agreement with the rotamer distribution from NMR experiment being for gt:gg:tg 38 : 53 : 9, respectively, with a proposed inter-residue O5'⋯HO6 hydrogen bond being predominant in the gg rotamer. Quantum mechanics methodology was used to calculate transglycosidic NMR 3JCH coupling constants, averaged over a conformational ensemble of structures representing various rotamers of exocyclic groups, in good to excellent agreement with Karplus-type relationships previously developed. Furthermore, 1H and 13C NMR chemical shifts were calculated using the same methodology and were found to be in excellent agreement with experimental data.

Temperature Accelerated Sliced Sampling to Probe Ligand Dissociation from Protein

Modeling ligand unbinding in proteins to estimate the free energy of binding and probing the mechanism presents several challenges. They primarily pertain to the entropic bottlenecks resulting from protein and solvent conformations. While exploring the unbinding processes using enhanced sampling techniques, very long simulations are required to sample all of the conformational states as the system gets trapped in local free energy minima along transverse coordinates. Here, we demonstrate that temperature accelerated sliced sampling (TASS) is an ideal approach to overcome some of the difficulties faced by conventional sampling methods in studying ligand unbinding. Using TASS, we study the unbinding of avibactam inhibitor molecules from the Class C β-lactamase (CBL) active site. Extracting CBL-avibactam unbinding free energetics, unbinding pathways, and identifying critical interactions from the TASS simulations are demonstrated.

First principles reaction discovery: from the Schrodinger equation to experimental prediction for methane pyrolysis

Our recent success in exploiting graphical processing units (GPUs) to accelerate quantum chemistry computations led to the development of the ab initio nanoreactor, a computational framework for automatic reaction discovery and kinetic model construction. In this work, we apply the ab initio nanoreactor to methane pyrolysis, from automatic reaction discovery to path refinement and kinetic modeling. Elementary reactions occurring during methane pyrolysis are revealed using GPU-accelerated ab initio molecular dynamics simulations. Subsequently, these reaction paths are refined at a higher level of theory with optimized reactant, product, and transition state geometries. Reaction rate coefficients are calculated by transition state theory based on the optimized reaction paths. The discovered reactions lead to a kinetic model with 53 species and 134 reactions, which is validated against experimental data and simulations using literature kinetic models. We highlight the advantage of leveraging local brute force and Monte Carlo sensitivity analysis approaches for efficient identification of important reactions. Both sensitivity approaches can further improve the accuracy of the methane pyrolysis kinetic model. The results in this work demonstrate the power of the ab initio nanoreactor framework for computationally affordable systematic reaction discovery and accurate kinetic modeling.

Improving Speed and Affordability without Compromising Accuracy: Standard Binding Free-Energy Calculations Using an Enhanced Sampling Algorithm, Multiple-Time Stepping, and Hydrogen Mass Repartitioning

Accurate evaluation of protein-ligand binding free energies in silico is of paramount importance for understanding the mechanisms of biological regulation and providing a theoretical basis for drug design and discovery. Based on a series of atomistic molecular dynamics simulations in an explicit solvent, using well-tempered metadynamics extended adaptive biasing force (WTM-eABF) as an enhanced sampling algorithm, the so-called "geometrical route" offers a rigorous theoretical framework for binding affinity calculations that match experimental values. However, although robust, this strategy remains expensive, requiring substantial computational time to achieve convergence of the simulations. Improving the efficiency of the geometrical route, while preserving its reliability through improved ergodic sampling, is, therefore, highly desirable. In this contribution, having identified the computational bottleneck of the geometrical route, to accelerate the calculations we combine (i) a longer time step for the integration of the equations of motion with hydrogen-mass repartitioning (HMR), and (ii) multiple time-stepping (MTS) for collective-variable and biasing-force evaluation. Altogether, we performed 50 independent WTM-eABF simulations in triplicate for the "physical" separation of the Abl kinase-SH3 domain:p41 complex, following different HMR and MTS schemes, while tuning, in distinct protocols, the parameters of the enhanced-sampling algorithm. To demonstrate the consistency and reliability of the results obtained with the best-performing setups, we carried out quintuple simulations. Furthermore, we demonstrated the transferability of our method to other complexes by triplicating a 200 ns separation simulation of nine chosen protocols for the MDM2-p53:NVP-CGM097 complex. [Holzer et al. J. Med. Chem. 2015, 58, 6348-6358.] Our results, based on an aggregate simulation time of 14.4 μs, allowed an optimal set of parameters to be identified, able to accelerate convergence by a factor of three without any noticeable loss of accuracy.

Ab Initio Metadynamics Simulations of Hexafluoroisopropanol Solvent Effects: Synergistic Role of Solvent H-Bonding Networks and Solvent-Solute C-H/π Interactions

The solvent effects in Friedel-Crafts cycloalkylation of epoxides and Cope rearrangement of aldimines were investigated by using ab initio molecular dynamics simulations. Explicit molecular treatments were applied for both reactants and solvents. The reaction mechanisms were elucidated via free energy calculations based on metadynamics simulations. The results reveal that both reactions proceed in a concerted fashion. Key solvent-substrate interactions are identified from the structures of transition states with explicit solvent molecules. The remarkable promotion effect of hexafluoroisopropanol solvent is ascribed to the synergistic effect of H-bonding networks and C-H/π interactions with substrates.

Ethanol Oxidation Reaction Mechanism on Gold Nanowires from Density Functional Theory

Thin gold nanowires (NWs) are materials that could be used as support in different chemical reactions. Using density functional theory (DFT) it was shown that NWs that form linear atomic chains (LACs) are suitable for stimulating chemical reactions. To this end, the oxidation reaction of ethanol supported on the LACs of Au-NWs was investigated. Two types of LACs were used for the study, one pure and the other with an oxygen impurity. The results showed that the oxygen atom in the LAC fulfills important functions throughout the reaction pathway. Before the chemical reaction, it was observed that the LAC with impurity gains structural stability, that is, the oxygen acts as an anchor for the gold atoms in the LAC. In addition, the LAC was shown to be sensitive to disturbances in its vicinity, which modifies its nucleophilic character. During the chemical reaction, the oxidation of ethanol occurs through two different reaction paths and in two stages, both producing acetaldehyde (CH₃ CHO). The different reaction pathways are a consequence of the presence of oxygen in the LAC (oxygen conditions the formation of reaction intermediates). In addition, the oxygen in the LAC also modifies the kinetic behavior in both reaction stages. It was observed that, by introducing an oxygen impurity in the LAC, the activation energy barriers decrease ∼69 % and ∼97 % in the first and second reaction stages, respectively.

A Multiple Proton Transfer Mechanism for the Charging Step of the Aminoacylation Reaction at the Active Site of Aspartyl tRNA Synthetase

Aspartyl-tRNA synthetase catalyzes the attachment of aspartic acid to its cognate tRNA by the aminoacylation reaction during the initiation of the protein biosynthesis process. In the second step of the aminoacylation reaction, known as the charging step, the aspartate moiety is transferred from aspartyl-adenylate to the 3'-OH of A76 of tRNA through a proton transfer process. We have investigated different pathways for the charging step through three separate QM/MM simulations combined with the enhanced sampling method of well-sliced metadynamics and found out the most feasible pathway for the reaction at the active site of the enzyme. In the charging reaction, both the phosphate group and the ammonium group after deprotonation can potentially act as a base for proton transfer in the substrate-assisted mechanism. We have considered three possible mechanisms involving different pathways of proton transfer, and only one of them is determined to be enzymatically feasible. The free energy landscape along reaction coordinates where the phosphate group acts as the general base showed that, in the absence of water, the barrier height is 52.6 kcal/mol. The free energy barrier is reduced to 39.7 kcal/mol when the active site water molecules are also treated quantum mechanically, thus allowing a water mediated proton transfer. The charging reaction involving the ammonium group of the aspartyl adenylate is found to follow a path where first a proton from the ammonium group moves to a water in the vicinity forming a hydronium ion (H₃O⁺) and NH₂ group. The hydronium ion subsequently passes the proton to the Asp233 residue, thus minimizing the chance of back proton transfer from hydronium to the NH₂ group. The neutral NH₂ group subsequently takes the proton from the O3' of A76 with a free energy barrier of 10.7 kcal/mol. In the next step, the deprotonated O3' makes a nucleophilic attack to the carbonyl carbon forming a tetrahedral transition state with a free energy barrier of 24.8 kcal/mol. Thus, the present work shows that the charging step proceeds through a multiple proton transfer mechanism where the amino group formed after deprotonation acts as the base to capture a proton from O3' of A76 rather than the phosphate group. The current study also shows the important role played by Asp233 in the proton transfer process.

The Electronic Structure of Genome Editors from the First Principles

Genome editing based on the CRISPR-Cas9 system has paved new avenues for medicine, pharmaceutics, biotechnology, and beyond. This article reports the role of first-principles (ab-initio) molecular dynamics (MD) in the CRISPR-Cas9 revolution, achieving a profound understanding of the enzymatic function and offering valuable insights for enzyme engineering. We introduce the methodologies and explain the use of ab-initio MD simulations to characterize the two-metal dependent mechanism of DNA cleavage in the RuvC domain of the Cas9 enzyme, and how a second catalytic domain, HNH, cleaves the target DNA with the aid of a single metal ion. A detailed description of how ab-initio MD is combined with free-energy methods - i.e., thermodynamic integration and metadynamics - to break and form chemical bonds is given, explaining the use of these methods to determine the chemical landscape and establish the catalytic mechanism in CRISPR-Cas9. The critical role of classical methods is also discussed, explaining theory and application of constant pH MD simulations, used to accurately predict the catalytic residues' protonation states. Overall, first-principles methods are shown to unravel the electronic structure of the Cas9 enzyme, providing valuable insights that can serve for the design of genome editing tools with improved catalytic efficiency or controllable activity.

Theoretical Calculations on Metal Catalysts Toward Water-Gas Shift Reaction: a Review

Water-gas shift (WGS) reaction offers a dominating path to hydrogen generation from fossil fuel, in which heterogeneous metal catalysts play a crucial part in this course. This review highlights and summarizes recent developments on theoretical calculations of metal catalysts developed to date, including surface structure (e. g., monometallic and polymetallic systems) and interface structure (e. g., supported catalysts and metal oxide composites), with special emphasis on the characteristics of crystal-face effect, alloying strategy, and metal-support interaction. A systematic summarization on reaction mechanism was performed, including redox mechanism, associative mechanism as well as hybrid mechanism; the development on chemical kinetics (e. g., molecular dynamics, kinetic Monte Carlo and microkinetic simulation) was then introduced. At the end, challenges associated with theoretical calculations on metal catalysts toward WGS reaction are discussed and some perspectives on the future advance of this field are provided.

Accurate Hellmann-Feynman forces from density functional calculations with augmented Gaussian basis sets

The Hellmann-Feynman (HF) theorem provides a way to compute forces directly from the electron density, enabling efficient force calculations for large systems through machine learning (ML) models for the electron density. The main issue holding back the general acceptance of the HF approach for atom-centered basis sets is the well-known Pulay force which, if naively discarded, typically constitutes an error upward of 10 eV/Å in forces. In this work, we demonstrate that if a suitably augmented Gaussian basis set is used for density functional calculations, the Pulay force can be suppressed, and HF forces can be computed as accurately as analytical forces with state-of-the-art basis sets, allowing geometry optimization and molecular dynamics to be reliably performed with HF forces. Our results pave a clear path forward for the accurate and efficient simulation of large systems using ML densities and the HF theorem.

Sarcin/Ricin Domain RNA Retains Its Structure Better Than A-RNA in Adaptively Biased Molecular Dynamics Simulations

Less than one in thirty of the RNA sequences transcribed in humans are translated into protein. The noncoding RNA (ncRNA) functions in catalysis, structure, regulation, and more. However, for the most part, these functions are poorly characterized. RNA is modular and described by motifs that include helical A-RNA with canonical Watson-Crick base-pairing as well as structures with only noncanonical base pairs. Understanding the structure and dynamics of motifs will aid in deciphering functions of specific ncRNAs. We present computational studies on a standard sarcin/ricin domain (SRD), citrus bark cracking viroid SRD, as well as A-RNA. We have applied enhanced molecular dynamics techniques that construct an inverse free-energy surface (iFES) determined by collective variables that monitor base-pairing and backbone conformation. Each SRD RNA is flanked on each side by A-RNA, allowing comparison of the behavior of these motifs in the same molecule. The RNA iFESs have single peaks, indicating that the combined motifs should denature as a single cohesive unit, rather than by regional melting. Local root-mean-square deviation (RMSD) analysis and communication propensity (CProp, variance in distances between residue pairs) reveal distinct motif properties. Our analysis indicates that the standard SRD is more stable than the viroid SRD, which is more stable than A-RNA. Base pairs at SRD to A-RNA transitions have limited flexibility. Application of CProp reveals extraordinary stiffness of the SRD, allowing residues on opposite sides of the motif to sense each other's motions.

Guided discovery of chemical reaction pathways with imposed activation

Computational power and quantum chemical methods have improved immensely since computers were first applied to the study of reactivity, but the de novo prediction of chemical reactions has remained challenging. We show that complex reaction pathways can be efficiently predicted in a guided manner using chemical activation imposed by geometrical constraints of specific reactive modes, which we term imposed activation (IACTA). Our approach is demonstrated on realistic and challenging chemistry, such as a triple cyclization cascade involved in the total synthesis of a natural product, a water-mediated Michael addition, and several oxidative addition reactions of complex drug-like molecules. Notably and in contrast with traditional hand-guided computational chemistry calculations, our method requires minimal human involvement and no prior knowledge of the products or the associated mechanisms. We believe that IACTA will be a transformational tool to screen for chemical reactivity and to study both by-product formation and decomposition pathways in a guided way.

Chalcogen Bond as a Factor Stabilizing Ligand Conformation in the Binding Pocket of Carbonic Anhydrase IX Receptor Mimic

It is postulated that the overexpression of Carbonic Anhydrase isozyme IX in some cancers contributes to the acidification of the extracellular matrix. It was proved that this promotes the growth and metastasis of the tumor. These observations have made Carbonic Anhydrase IX an attractive drug target. In the light of the findings and importance of the glycoprotein in the cancer treatment, we have employed quantum-chemical approaches to study non-covalent interactions in the binding pocket. As a ligand, the acetazolamide (AZM) molecule was chosen, being known as a potential inhibitor exhibiting anticancer properties. First-Principles Molecular Dynamics was performed to study the chalcogen and other non-covalent interactions in the AZM ligand and its complexes with amino acids forming the binding site. Based on Density Functional Theory (DFT) and post-Hartree-Fock methods, the metric and electronic structure parameters were described. The Non-Covalent Interaction (NCI) index and Atoms in Molecules (AIM) methods were applied for qualitative/quantitative analyses of the non-covalent interactions. Finally, the AZM-binding pocket interaction energy decomposition was carried out. Chalcogen bonding in the AZM molecule is an important factor stabilizing the preferred conformation. Free energy mapping via metadynamics and Path Integral molecular dynamics confirmed the significance of the chalcogen bond in structuring the conformational flexibility of the systems. The developed models are useful in the design of new inhibitors with desired pharmacological properties.