AtmoSpec-A Tool to Calculate Photoabsorption Cross-Sections for Atmospheric Volatile Organic Compounds.

Characterizing the photolysis processes undergone by transient volatile organic compounds (VOCs) in the troposphere requires the knowledge of their photoabsorption cross-section-quantities often challenging to determine experimentally, particularly due to the reactivity of these molecules. We present a computational tool coined AtmoSpec, which can predict a quantitative photoabsorption cross-section for volatile organic compounds by using computational photochemistry. The user enters the molecule of interest as a SMILES code and, after selecting a level of theory for the electronic structure (and waiting for the calculations to take place), is presented with a photoabsorption cross-section for the low-energy conformers and an estimate of the photolysis rate coefficient for different standardized actinic fluxes. More specifically, AtmoSpec is an automated workflow for the nuclear ensemble approach, an efficient technique to approximate the absolute intensities and excitation wavelengths of a photoabsorption cross-section for a molecule in the gas phase of interest in atmospheric chemistry and astrochemistry. This work provides background information on the nuclear ensemble approach, a guided example of a typical AtmoSpec calculation, details about the architecture of the code, and the current limitations and future developments of this tool.

Predicting the photodynamics of cyclobutanone triggered by a laser pulse at 200 nm and its MeV-UED signals-A trajectory surface hopping and XMS-CASPT2 perspective.

This work is part of a prediction challenge that invited theoretical/computational chemists to predict the photochemistry of cyclobutanone in the gas phase, excited at 200 nm by a laser pulse, and the expected signal that will be recorded during a time-resolved megaelectronvolt ultrafast electron diffraction (MeV-UED). We present here our theoretical predictions based on a combination of trajectory surface hopping with XMS-CASPT2 (for the nonadiabatic molecular dynamics) and Born-Oppenheimer molecular dynamics with MP2 (for the athermal ground-state dynamics following internal conversion), coined (NA+BO)MD. The initial conditions were sampled from Born-Oppenheimer molecular dynamics coupled to a quantum thermostat. Our simulations indicate that the main photoproducts after 2 ps of dynamics are CO + cyclopropane (50%), CO + propene (10%), and ethene and ketene (34%). The photoexcited cyclobutanone in its second excited electronic state S2 can follow two pathways for its nonradiative decay: (i) a ring-opening in S2 and a subsequent rapid decay to the ground electronic state, where the photoproducts are formed, or (ii) a transfer through a closed-ring conical intersection to S1, where cyclobutanone ring opens and then funnels to the ground state. Lifetimes for the photoproduct and electronic populations were determined. We calculated a stationary MeV-UED signal [difference pair distribution function-ΔPDF(r)] for each (interpolated) pathway as well as a time-resolved signal [ΔPDF(r,t) and ΔI/I(s,t)] for the full swarm of (NA+BO)MD trajectories. Furthermore, our analysis provides time-independent basis functions that can be used to fit the time-dependent experimental UED signals [both ΔPDF(r,t) and ΔI/I(s,t)] and potentially recover the population of photoproducts. We also offer a detailed analysis of the limitations of our model and their potential impact on the predicted experimental signals.

Deciphering the Influence of Ground-State Distributions on the Calculation of Photolysis Observables.

Nonadiabatic molecular dynamics offers a powerful tool for studying the photochemistry of molecular systems. Key to any nonadiabatic molecular dynamics simulation is the definition of its initial conditions (ICs), ideally representing the initial molecular quantum state of the system of interest. In this work, we provide a detailed analysis of how ICs may influence the calculation of experimental observables by focusing on the photochemistry of methylhydroperoxide (MHP), the simplest and most abundant organic peroxide in our atmosphere. We investigate the outcome of trajectory surface hopping simulations for distinct sets of ICs sampled from different approximate quantum distributions, namely harmonic Wigner functions and ab initio molecular dynamics using a quantum thermostat (QT). Calculating photoabsorption cross-sections, quantum yields, and translational kinetic energy maps from the results of these simulations reveals the significant effect of the ICs, in particular when low-frequency (∼ a few hundred cm-1) normal modes are connected to the photophysics of the molecule. Overall, our results indicate that sampling ICs from ab initio molecular dynamics using a QT is preferable for flexible molecules with photoactive low-frequency modes. From a photochemical perspective, our nonadiabatic dynamics simulations offer an explanation for a low-energy tail observed at high excitation energy in the translational kinetic energy map of MHP.

Jahn-Teller effects in initial and final states: high-resolution X-ray absorption, photoelectron and Auger spectroscopy of allene.

Carbon K-edge resonant Auger spectra of gas-phase allene following excitation of the pre-edge 1s → π* transitions are presented and analysed with the support of EOM-CCSD/cc-pVTZ calculations. X-Ray absorption (XAS), X-ray photoelectron (XPS), valence band and non-resonant Auger spectra are also reanalysed with a series of computational approaches. The results presented demonstrate the importance of including nuclear ensemble effects for simulating X-ray observables and as an effective strategy for capturing Jahn-Teller effects in spectra.

Extending the Applicability of the Multiple-Spawning Framework for Nonadiabatic Molecular Dynamics.

Ab initio multiple-spawning (AIMS) describes the nonadiabatic dynamics of molecules by expanding nuclear wave functions in a basis of traveling multidimensional Gaussians called trajectory basis functions (TBFs). New TBFs can be spawned whenever nuclear amplitude is transferred between electronic states due to nonadiabatic transitions. While the adaptive size of the TBF basis grants AIMS its characteristic accuracy in describing nonadiabatic processes, it also leads to a fast and uncontrolled growth of the number of TBFs, penalizing computational efficiency. A different flavor of AIMS, called AIMS with informed stochastic selections (AIMSWISS), has recently been proposed to reduce the number of TBFs dramatically. Herein, we test the performance of AIMSWISS for a series of challenging nonadiabatic processes─photodynamics of two-dimensional model systems, 1,2-dithiane and chromium (0) hexacarbonyl─and show that this method is robust and extends the range of molecular systems that can be simulated within the multiple-spawning framework.

Calculating Photoabsorption Cross-Sections for Atmospheric Volatile Organic Compounds.

Characterizing the photochemical reactivity of transient volatile organic compounds (VOCs) in our atmosphere begins with a proper understanding of their abilities to absorb sunlight. Unfortunately, the photoabsorption cross-sections for a large number of transient VOCs remain unavailable experimentally due to their short lifetime or high reactivity. While structure-activity relationships (SARs) have been successfully employed to estimate the unknown photoabsorption cross-sections of VOCs, computational photochemistry offers another promising strategy to predict not only the vertical electronic transitions of a given molecule but also the width and shape of the bands forming its absorption spectrum. In this work, we focus on the use of the nuclear ensemble approach (NEA) to determine the photoabsorption cross-section of four exemplary VOCs, namely, acrolein, methylhydroperoxide, 2-hydroperoxy-propanal, and (microsolvated) pyruvic acid. More specifically, we analyze the influence that different strategies for sampling the ground-state nuclear density-Wigner sampling and ab initio molecular dynamics with a quantum thermostat-can have on the simulated absorption spectra. We highlight the potential shortcomings of using uncoupled harmonic modes within Wigner sampling of nuclear density to describe flexible or microsolvated VOCs and some limitations of SARs for multichromophoric VOCs. Our results suggest that the NEA could constitute a powerful tool for the atmospheric community to predict the photoabsorption cross-section for transient VOCs.

Hamiltonian-Reservoir Replica Exchange and Machine Learning Potentials for Computational Organic Chemistry.

This work combines a machine learning potential energy function with a modular enhanced sampling scheme to obtain statistically converged thermodynamical properties of flexible medium-size organic molecules at high ab initio level. We offer a modular environment in the python package MORESIM that allows custom design of replica exchange simulations with any level of theory including ML-based potentials. Our specific combination of Hamiltonian and reservoir replica exchange is shown to be a powerful technique to accelerate enhanced sampling simulations and explore free energy landscapes with a quantum chemical accuracy unattainable otherwise (e.g., DLPNO-CCSD(T)/CBS quality). This engine is used to demonstrate the relevance of accessing the ab initio free energy landscapes of molecules whose stability is determined by a subtle interplay between variations in the underlying potential energy and conformational entropy (i.e., a bridged asymmetrically polarized dithiacyclophane and a widely used organocatalyst) both in the gas phase and in solution (implicit solvent).

Mechanisms of fluorescence quenching in prototypical aggregation-induced emission systems: excited state dynamics with TD-DFTB.

A recent implementation of time-dependent tight-binding density functional theory is employed in excited state molecular dynamics for the investigation of the fluorescence quenching mechanism in 3 prototypical aggregation-induced emission systems. An assessment of the accuracy of the electronic structure method is done by comparison with previous theoretical work while dynamics simulations were extended to the condensed phase to obtain excited state lifetimes comparable to experiment. A thorough investigation is done on tetraphenylethylene in order to resolve the on-going debate on the role of specific deactivation mechanisms. Both gas phase and solvent dynamics were computed for fulvene and silole derivatives.

Two Tryptophans Are Better Than One in Accelerating Electron Flow through a Protein.

We have constructed and structurally characterized a Pseudomonas aeruginosa azurin mutant Re126WWCuI , where two adjacent tryptophan residues (W124 and W122, indole separation 3.6-4.1 Å) are inserted between the CuI center and a Re photosensitizer coordinated to the imidazole of H126 (ReI(H126)(CO)3(4,7-dimethyl-1,10-phenanthroline)+). CuI oxidation by the photoexcited Re label (*Re) 22.9 Å away proceeds with a ∼70 ns time constant, similar to that of a single-tryptophan mutant (∼40 ns) with a 19.4 Å Re-Cu distance. Time-resolved spectroscopy (luminescence, visible and IR absorption) revealed two rapid reversible electron transfer steps, W124 → *Re (400-475 ps, K 1 ≅ 3.5-4) and W122 → W124•+ (7-9 ns, K 2 ≅ 0.55-0.75), followed by a rate-determining (70-90 ns) CuI oxidation by W122•+ ca. 11 Å away. The photocycle is completed by 120 µs recombination. No photochemical CuI oxidation was observed in Re126FWCuI , whereas in Re126WFCuI , the photocycle is restricted to the ReH126W124 unit and CuI remains isolated. QM/MM/MD simulations of Re126WWCuI indicate that indole solvation changes through the hopping process and W124 → *Re electron transfer is accompanied by water fluctuations that tighten W124 solvation. Our finding that multistep tunneling (hopping) confers a ∼9000-fold advantage over single-step tunneling in the double-tryptophan protein supports the proposal that hole-hopping through tryptophan/tyrosine chains protects enzymes from oxidative damage.

Competition between proton transfer and intermolecular Coulombic decay in water.

Intermolecular Coulombic decay (ICD) is a ubiquitous relaxation channel of electronically excited states in weakly bound systems, ranging from dimers to liquids. As it is driven by electron correlation, it was assumed that it will dominate over more established energy loss mechanisms, for example fluorescence. Here, we use electron-electron coincidence spectroscopy to determine the efficiency of the ICD process after 2a1 ionization in water clusters. We show that this efficiency is surprisingly low for small water clusters and that it gradually increases to 40-50% for clusters with hundreds of water units. Ab initio molecular dynamics simulations reveal that proton transfer between neighboring water molecules proceeds on the same timescale as ICD and leads to a configuration in which the ICD channel is closed. This conclusion is further supported by experimental results from deuterated water. Combining experiment and theory, we infer an intrinsic ICD lifetime of 12-52 fs for small water clusters.

On the importance of initial conditions for excited-state dynamics.

Photodynamical simulations are increasingly used to explore photochemical mechanisms and interpret laser experiments. The vast majority of ab initio excited-state simulations are performed within semiclassical, trajectory-based approaches. Apart from underlying electronic-structure theory, the reliability of simulations is controlled by a selection of initial conditions for the classical trajectories. We discuss appropriate choices of initial conditions for simulations of different experimental arrangements: dynamics initiated by continuum-wave (CW) laser fields or triggered by ultrashort laser pulses. We introduce a new technique, CW-sampling, to treat the former case, based on the ideas of importance sampling, combined with the quantum thermostat approach based on the Generalized Langevin Equation (GLE) that allows for efficient sampling of both position and momentum space. The CW-sampling is particularly important for photodynamical processes initiated by absorption at the tail of the UV absorption spectrum. We also emphasize the importance of non-Condon effects for the dynamics. We demonstrate the performance of our approach on the photodissociation of the CF2Cl2 molecule (Freon CFC-12). A quantitative agreement with the experimental data is achieved with the use of empirical correlation energy correction (CEC) factor on top of FOMO-CASCI potential energy surfaces.

Nonadiabatic Ab Initio Molecular Dynamics with the Floating Occupation Molecular Orbital-Complete Active Space Configuration Interaction Method.

We show that the floating occupation molecular orbital complete active space configuration interaction (FOMO-CASCI) method is a promising alternative to the widely used complete active space self-consistent field (CASSCF) method in direct nonadiabatic dynamics simulations. We have simulated photodynamics of three archetypal molecules in photodynamics: ethylene, methaniminium cation, and malonaldehyde. We compared the time evolution of electronic populations and reaction mechanisms as revealed by the FOMO-CASCI and CASSCF approaches. Generally, the two approaches provide similar results. Some dynamical differences are observed, but these can be traced back to energetically minor differences in the potential energy surfaces. We suggest that the FOMO-CASCI method represents, due to its efficiency and stability, a promising approach for direct ab initio dynamics in the excited state.

Aqueous Solution Chemistry of Ammonium Cation in the Auger Time Window.

We report on chemical reactions triggered by core-level ionization of ammonium ([Formula: see text]) cation in aqueous solution. Based on a combination of photoemission experiments from a liquid microjet and high-level ab initio simulations, we identified simultaneous single and double proton transfer occurring on a very short timescale spanned by the Auger-decay lifetime. Molecular dynamics simulations indicate that the proton transfer to a neighboring water molecule leads to essentially complete formation of H3O+ (aq) and core-ionized ammonia [Formula: see text](aq) within the ~7 fs lifetime of the nitrogen 1s core hole. A second proton transfer leads to a transient structure with the proton shared between the remaining NH2 moiety and another water molecule in the hydration shell. These ultrafast proton transfers are stimulated by very strong hydrogen bonds between the ammonium cation and water. Experimentally, the proton transfer dynamics is identified from an emerging signal at the high-kinetic energy side of the Auger-electron spectrum in analogy to observations made for other hydrogen-bonded aqueous solutions. The present study represents the most pronounced charge separation observed upon core ionization in liquids so far.

Modeling Liquid Photoemission Spectra: Path-Integral Molecular Dynamics Combined with Tuned Range-Separated Hybrid Functionals.

We present a computational protocol for modeling valence photoemission spectra of liquids. We use water as an experimentally well-characterized model system, and we represent its liquid state by larger finite-sized droplets. The photoemission spectrum is evaluated for an ensemble of structures along molecular dynamics simulations. The nuclear quantum effects are accounted for by ab initio based path-integral molecular dynamics simulations that are greatly accelerated with the so-called colored noise thermostat (PI+GLE) method. The ionization energies for the valence electrons are evaluated as orbital energies of optimally tuned range-separated hybrid functionals (OT-RSH). This approach provides Koopmans-type ionization energies including relaxation energy. We show that the present protocol can quantitatively describe the valence photoemission spectrum of liquid water, i.e., the positions, shapes, and widths of the photoemission peaks. With the PI+GLE simulations, even the subtle isotope effects that have been recently observed experimentally can be modeled. The electronic properties of finite-sized droplets are shown to converge rapidly to those of liquids. We discuss the importance of proper tuning of the range-separation parameter in OT-RSH as well as possible sources of error in our simulations. The present approach seems to be a viable route to modeling photoemission spectra of liquids, especially in conjunction with efficient implementation of density functional methods on graphical processing units.

On the Performance of Optimally Tuned Range-Separated Hybrid Functionals for X-ray Absorption Modeling.

We investigate the performance of optimally tuned range-separated hybrid functionals (OT-RSH) for modeling X-ray absorption spectra (XAS) of a benchmark set of simple molecules (water, ammonia, methane, hydrogen peroxide, hydrazine, and ethane), using time-dependent density functional theory (TDDFT). Spectra were simulated within the Path Integral based Reflection Principle methodology. Relative intensities, peak positions, and widths were compared with available experimental data. We show that the OT-RSH approach outperforms empirically parametrized functionals in terms of relative peak positions and intensities. Furthermore, we investigate the effect of geometry specific tuning where the range separation parameter is optimized for each geometry. Finally, we propose a simple correction scheme allowing for calculations of XAS on the absolute energy scale using the OT-RSH approach combined with ΔSCF/TDDFT-based calculations of core ionization energies.

Control of X-ray Induced Electron and Nuclear Dynamics in Ammonia and Glycine Aqueous Solution via Hydrogen Bonding.

Recently, a new family of autoionization processes has been identified in aqueous phases. The processes are initiated by core-electron ionization of a solute molecule and involve proton transfer along the solute-solvent hydrogen bond. As a result, short-lived singly charged cations form with structures sharing a proton between solute and solvent molecules. These molecular transients decay by autoionization, which creates reactive dicationic species with the positive charges delocalized over the entire molecular entity. Here, we investigate the ultrafast electron and nuclear dynamics following the core ionization of hydrated ammonia and glycine. Both molecules serve as models for exploring the possible role of the nonlocal relaxation processes in the chemical reactivity at the interface between, for instance, a protein surface and aqueous solution. The nature of the postionization dynamical processes is revealed by high-accuracy Auger-electron spectroscopy measurements on liquid microjets in vacuum. The proton-transfer-mediated processes are identified by electron signals in the high-energy tail of the Auger spectra with no analogue in the Auger spectra of the corresponding gas-phase molecule. This high-energy tail is suppressed for deuterated molecules. Such an isotope effect is found to be smaller for aqueous ammonia as compared to the hydrated H2O molecule, wherein hydrogen bonds are strong. An even weaker hydrogen bonding for the hydrated amino groups in glycine results in a negligibly small proton transfer. The dynamical processes and species formed upon the nitrogen-1s core-level ionization are interpreted using methods of quantum chemistry and molecular dynamics. With the assistance of such calculations, we discuss the conditions for the proton-transfer-mediated relaxation processes to occur. We also consider the solvent librational dynamics as an alternative intermolecular ultrafast relaxation pathway. In addition, we provide experimental evidence for the umbrella-type motion in aqueous ammonia upon core ionization. This intramolecular channel proceeds in parallel with intermolecular relaxation processes in the solution.

Clustering and photochemistry of freon CF2Cl2 on argon and ice nanoparticles.

The photochemistry of CF2Cl2 molecules deposited on argon and ice nanoparticles was investigated. The clusters were characterized via electron ionization mass spectrometry, and the photochemistry was revealed by the Cl fragment velocity map imaging after the CF2Cl2 photodissociation at 193 nm. The complex molecular beam experiment was complemented by ab initio calculations. The (CF2Cl2)n clusters were generated in a coexpansion with Ar buffer gas. The photodissociation of molecules in the (CF2Cl2)n clusters yields predominantly Cl fragments with zero kinetic energy: caging. The CF2Cl2 molecules deposited on large argon clusters in a pickup experiment are highly mobile and coagulate to form the (CF2Cl2)n clusters on ArN. The photodissociation of the CF2Cl2 molecules and clusters on ArN leads to the caging of the Cl fragment. On the other hand, the CF2Cl2 molecules adsorbed on the (H2O)N ice nanoparticles do not form clusters, and no Cl fragments are observed from their photodissociation. Since the CF2Cl2 molecule was clearly adsorbed on (H2O)N, the missing Cl signal is interpreted in terms of surface orientation, possibly via the so-called halogen bond and/or embedding of the CF2Cl2 molecule on the disordered surface of the ice nanoparticles.

Reaction selectivity in an ionized water dimer: nonadiabatic ab initio dynamics simulations.

We study dynamical processes following water dimer ionization. The nonadiabatic dynamical simulations of the water dimer radical cation are performed using a surface hopping technique and a Complete Active Space-Self Consistent Field (CASSCF) method for the description of electronic structure. The main goal of this study is to find out whether a state-dependent reactivity is observed for the water dimer radical cation. We provide a detailed mapping of the potential energy surfaces (PESs) in the relevant coordinates for different electronic states. Dynamical patterns are discussed on the basis of static PES cuts and available experimental data. As a product of the reaction, we observed either proton transferred structure (H3O(+)···OH˙) or various dissociated structures (H3O(+) + OH˙, H2O˙(+) + H2O, H˙ + OH˙ + H2O˙(+)). The relative yields are controlled by the populated electronic state of the radical cation. The proton transfer upon the HOMO electron ionization is an ultrafast process, taking less than 100 fs, in cases of higher energy ionization the dynamical processes occur on longer timescales (200-300 fs). We also discuss the implications of our simulations for the efficiency of the recently identified intermolecular coulomb decay (ICD) process in the water dimer.

Extensive molecular dynamics simulations showing that canonical G8 and protonated A38H+ forms are most consistent with crystal structures of hairpin ribozyme.

The hairpin ribozyme is a prominent member of the group of small catalytic RNAs (RNA enzymes or ribozymes) because it does not require metal ions to achieve catalysis. Biochemical and structural data have implicated guanine 8 (G8) and adenine 38 (A38) as catalytic participants in cleavage and ligation catalyzed by the hairpin ribozyme, yet their exact role in catalysis remains disputed. To gain insight into dynamics in the active site of a minimal self-cleaving hairpin ribozyme, we have performed extensive classical, explicit-solvent molecular dynamics (MD) simulations on time scales of 50-150 ns. Starting from the available X-ray crystal structures, we investigated the structural impact of the protonation states of G8 and A38, and the inactivating A-1(2'-methoxy) substitution employed in crystallography. Our simulations reveal that a canonical G8 agrees well with the crystal structures while a deprotonated G8 profoundly distorts the active site. Thus MD simulations do not support a straightforward participation of the deprotonated G8 in catalysis. By comparison, the G8 enol tautomer is structurally well tolerated, causing only local rearrangements in the active site. Furthermore, a protonated A38H(+) is more consistent with the crystallography data than a canonical A38. The simulations thus support the notion that A38H(+) is the dominant form in the crystals, grown at pH 6. In most simulations, the canonical A38 departs from the scissile phosphate and substantially perturbs the structures of the active site and S-turn. Yet, we occasionally also observe formation of a stable A-1(2'-OH)...A38(N1) hydrogen bond, which documents the ability of the ribozyme to form this hydrogen bond, consistent with a potential role of A38 as general base catalyst. The presence of this hydrogen bond is, however, incompatible with the expected in-line attack angle necessary for self-cleavage, requiring a rapid transition of the deprotonated 2'-oxyanion to a position more favorable for in-line attack after proton transfer from A-1(2'-OH) to A38(N1). The simulations revealed a potential force field artifact, occasional but irreversible formation of "ladder-like", underwound A-RNA structure in one of the external helices. Although it does not affect the catalytic center of the hairpin ribozyme, further studies are under way to better assess possible influence of such force field behavior on long RNA simulations.

Performance of Molecular Mechanics Force Fields for RNA Simulations: Stability of UUCG and GNRA Hairpins.

The RNA hairpin loops represent important RNA topologies with indispensable biological functions in RNA folding and tertiary interactions. 5'-UNCG-3' and 5'-GNRA-3' RNA tetraloops are the most important classes of RNA hairpin loops. Both tetraloops are highly structured with characteristic signature three-dimensional features and are recurrently seen in functional RNAs and ribonucleoprotein particles. Explicit solvent molecular dynamics (MD) simulation is a computational technique which can efficiently complement the experimental data and provide unique structural dynamics information on the atomic scale. Nevertheless, the outcome of simulations is often compromised by imperfections in the parametrization of simplified pairwise additive empirical potentials referred to also as force fields. We have pointed out in several recent studies that a force field description of single-stranded hairpin segments of nucleic acids may be particularly challenging for the force fields. In this paper, we report a critical assessment of a broad set of MD simulations of UUCG, GAGA, and GAAA tetraloops using various force fields. First, we utilized the three widely used variants of Cornell et al. (AMBER) force fields known as ff94, ff99, and ff99bsc0. Some simulations were also carried out with CHARMM27. The simulations reveal several problems which show that these force fields are not able to retain all characteristic structural features (structural signature) of the studied tetraloops. Then we tested four recent reparameterizations of glycosidic torsion of the Cornell et al. force field (two of them being currently parametrized in our laboratories). We show that at least some of the new versions show an improved description of the tetraloops, mainly in the syn glycosidic torsion region of the UNCG tetraloop. The best performance is achieved in combination with the bsc0 parametrization of the α/γ angles. Another critically important region to properly describe RNA molecules is the anti/high-anti region of the glycosidic torsion, where there are significant differences among the tested force fields. The tetraloop simulations are complemented by simulations of short A-RNA stems, which are especially sensitive to an appropriate description of the anti/high-anti region. While excessive accessibility of the high-anti region converts the A-RNA into a senseless "ladder-like" geometry, excessive penalization of the high-anti region shifts the simulated structures away from typical A-RNA geometry to structures with a visibly underestimated inclination of base pairs with respect to the helical axis.