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Mid-infrared vibrational spectra of He–HN+2 and He2–HN+2 have been recorded by monitoring their photofragmentation in a tandem mass spectrometer. For He–HN+2 three rotationally resolved bands are seen: the fundamental ν1 transition (N–H stretch) at 3158.419±0.009 cm-1, the ν1+νb combination band (N–H stretch plus intermolecular bend) at 3254.671±0.050 cm-1, and the ν1+νs combination band (N–H stretch plus intermolecular stretch) at 3321.466±0.050 cm-1. The spectroscopic data facilitate the development of approximate one-dimensional radial intermolecular potentials relevant to the collinear bonding of He to HN+2 in its (000) and (100) vibrational states. These consist of a short range potential derived from an RKR inversion of the spectroscopic data, together with a long range polarization potential generated by considering the interaction between the He atom and a set of multipoles distributed on the HN+2 nuclei. The following estimates for binding energies are obtained: D0″=378 cm-1 [He+HN+2(000)], and D0′=431 cm-1 [He+HN+2(100)]. While the ν1 band of He2–HN+2 is not rotationally resolved, the fact that it is barely shifted from the corresponding band of He–HN+2 suggests that the trimer possesses a structure in which one of the He atoms occupies a linear proton-bound position forming a He–HN+2 core, to which a second less strongly bound He is attached. © 1996 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Presents a method for constructing computationally cheap adiabatically corrected potential energy surfaces (PES) for intermolecular vibrational states. Reproduction of published experimental data for previous vibrational states; Comparison made between a set of intermolecular PES with a chemical core frozen into the equilibrium geometry.

The rates of rotational transitions for HCO+, the most abundant ion in interstellar space, induced by collision with helium are obtained for temperatures ranging from 10 to 80 K. The calculations are based on a new potential energy surface for the He–HCO+ interaction and on a scattering matrix whose accuracy was checked by pressure broadening and shift measurements. The rates decrease for increasing values of j and , with a temperature trend depending on the energy involved in the transitions: if it is small, the rates are almost constant, while an increase with T is found for other cases. Comparison with previous and less accurate results shows an agreement within 50 per cent. Comparison between state-to-state and pressure broadening cross-sections allows us to discuss importance and influence of elastic and inelastic collisions. [ABSTRACT FROM AUTHOR]

Using a recoupling technique with close-coupling spin-free calculations de-excitation rate coefficients are obtained among hyperfine transitions for He colliding with N2H+. A recently determined potential energy surface suitable for scattering calculations is used to investigate rate coefficients for temperatures between 5 and 50 K, and for the seven lowest rotational levels of N2H+. Fitting functions are provided for the Maxwellian averaged opacity tensors and for the rotational de-excitation collisional rate coefficients. The fitting functions for the opacity tensors can be used to calculate hyperfine (de)-excitation rate coefficients among elastic and inelastic rotational levels, and among the corresponding magnetic sublevels of the hyperfine structure. Certain dynamical approximations are investigated and found to be invalid. [ABSTRACT FROM AUTHOR]

A new potential energy surface for the molecular ion He--H[sub 2][sup +] is used to predict microwave transitions that may be observable in environments such as circumstellar envelopes and planetary nebulae. For the vibrational ground state, transitions are predicted at wavelengths of 1215, 608, 405, 304, 244, 203, 175, 154, 137 and 124 μ m. [ABSTRACT FROM AUTHOR]

The intermolecular potential energy surface of the electronic ground state of the ammonium-argon ionic dimer, NH[sub 4] [sup +] -Ar, is calculated by ab initiomethods using different levels of theory (MP2, MP4) and basis sets (aug-cc-pVXZ, X = D/T/Q). The deformation of the ammonium ion in the complex is shown to be small and its geometry is therefore fixed in these calculations to the tetrahedral structure optimized for the bare ion. The global minimum of the potential corresponds to a proton-bound structure with C[sub 3] symmetry (Rapproximately 3:4 A, Dapproximately 950cm[sup -1] ) and the barrier to internal rotation between the four equivalent minima is around 200cm[sup -1] . The three-dimensional potential is expanded in tetrahedral harmonics whose radially dependent coefficients, V(R), are compared for the considered levels of theory. The rotation-intermolecular vibration Hamiltonian is solved using a two-dimensional fixed-Rrepresentation of the calculated potentials, Vequals V(R), where the effective intermolecular separation, R[sup eff] , is determined from the experimental rotational constants of the complex. The accuracy of these parametrized potential energy surfaces is judged by their ability to reproduce the hindered rotor subband structure in the experimental upsilon[sub 3] (t[sub 2] ) infrared band of the complex. The simulations using the potentials calculated at the MP2/aug-cc-pVTZ or higher levels of theory reproduce the coarse structure of the experimental spectrum well. Further improvement could be achieved by least-squares fitting the potential parameters to the observed subband positions. The fitted V[sub 3] and V[sub 4] parameters remain in close agreement with those determined from the ab initiocalculations but the anisotropy of the potential is significantly different from that in a previous least-squares fit of V[sub 3] alone. [ABSTRACT FROM AUTHOR]

Rotational and vibrational energy relaxation (RER and VER) of N2O embedded in xenon and SF6 environments ranging from the gas phase to the liquid, including the supercritical regime, is studied at a molecular level. Calibrated intermolecular interactions from high-level electronic structure calculations, validated against experiments for the pure solvents, were used to carry out classical molecular dynamics simulations corresponding to experimental state points for near-critical isotherms. The computed RER rates in low-density solvents of krotXe=(3.67±0.25)×1010 s-1 M-1 and krotSF6=(1.25±0.12)×1011 s-1 M-1 compare well with the rates determined by the analysis of two-dimensional infrared experiments. Simulations find that an isolated binary collision description is successful up to solvent concentrations of ∼4 M. For higher densities, including the supercritical regime, the simulations do not correctly describe RER, probably due to the neglect of solvent-solute coupling in the analysis of the rotational motion. For VER, the near-quantitative agreement between simulations and pump-probe experiments captures the solvent density-dependent trends., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

Parametrizing energy functions for ionic systems can be challenging. Here, the total energy function for an eutectic system consisting of water, SCN - , K + and acetamide is improved vis-a-vis experimentally measured properties. Given the importance of electrostatic interactions, two different types of models are considered: the first (model M0 ) uses atom-centered multipole whereas the other two (models M1 and M2 ) are based on fluctuating minimal distributed charges (fMDCM) that respond to geometrical changes of SCN - . The Lennard-Jones parameters of the anion are adjusted to best reproduce experimentally known hydration free energies and densities, which are matched to within a few percent for the final models irrespective of the electrostatic model. Molecular dynamics simulations of the eutectic mixtures with varying water content (between 0 and 100%) yield radial distribution functions and frequency correlation functions for the CN-stretch vibration. Comparison with experiments indicates that models based on fMDCM are considerably more consistent than those using multipoles. Computed viscosities from models M1 and M2 are within 30% of measured values and their change with increasing water content is consistent with experiments. This is not the case for model M0 .

Since its inception nearly a half century ago, CHARMM has been playing a central role in computational biochemistry and biophysics. Commensurate with the developments in experimental research and advances in computer hardware, the range of methods and applicability of CHARMM have also grown. This review summarizes major developments that occurred after 2009 when the last review of CHARMM was published. They include the following: new faster simulation engines, accessible user interfaces for convenient workflows, and a vast array of simulation and analysis methods that encompass quantum mechanical, atomistic, and coarse-grained levels, as well as extensive coverage of force fields. In addition to providing the current snapshot of the CHARMM development, this review may serve as a starting point for exploring relevant theories and computational methods for tackling contemporary and emerging problems in biomolecular systems. CHARMM is freely available for academic and nonprofit research at https://academiccharmm.org/program.

The atom-exchange and atomization dissociation dynamics for the N( 4 S) + N 2 ( 1 Σ g + ) reaction are studied using a reproducing kernel Hilbert space (RKHS)-based, global potential energy surface (PES) at the MRCI-F12/aug-cc-pVTZ-F12 level of theory (MRCI, multireference configuration interaction). For the atom exchange reaction (N A N B + N C → N A N C + N B ), computed thermal rates and their temperature dependence from quasi-classical trajectory (QCT) simulations agree to within error bars with the available experiments. Companion QCT simulations using a recently published CASPT2-based PES confirm these findings. For the atomization reaction, leading to three N( 4 S) atoms, the computed rates from the RKHS-PES overestimate the experimentally reported rates by 1 order of magnitude, whereas those from the permutationally invariant polynomial (PIP)-PES agree favorably, and the T dependence of both computations is consistent with the experiment. These differences can be traced back to the different methods and basis sets used. The lifetime of the metastable N 3 molecule is estimated to be ∼200 fs depending on the initial state of the reactants. Finally, neural-network-based exhaustive state-to-distribution models are presented using both PESs for the atom exchange reaction. These models will be instrumental for a broader exploration of the reaction dynamics of air.

A kernel-based method (kernelized minimal distributed charge model (kMDCM)) to represent the molecular electrostatic potential (ESP) in terms of off-center point charges is introduced. The positions of the charges adapt to the molecular geometry and allow the description of intramolecular charge flow. Using Gaussian kernels and atom-atom distances as the features, the ESPs for water and methanol are shown to improve by at least a factor of 2 compared with point charge models fit to an ensemble of structures. The conformationally fluctuating molecular dipole moment of water is reproduced almost twice as accurately using kMDCM compared with static PCs, despite not fitting to the dipole directly. The role of hyperparameters in the kernelization is investigated and their implication on model performance and simulation stability is discussed. Combining kMDCM for the electrostatics and reproducing kernels for the bonded terms allows energy-conserving simulations of 2000 water molecules with periodic boundary conditions on the nanosecond time scale. These MD simulations sample geometries outside the training set but remain stable, which demonstrates the robustness of the model and its implementation.

The impact of targeted replacement of individual terms in empirical force fields is quantitatively assessed for pure water, dichloromethane (CH   2 Cl   2 ), and solvated K   + and Cl   - ions. For the electrostatic interactions, point charges (PCs) and machine learning (ML)-based minimally distributed charges (MDCM) fitted to the molecular electrostatic potential are evaluated together with electrostatics based on the Coulomb integral. The impact of explicitly including second-order terms is investigated by adding a fragment molecular orbital (FMO)-derived polarization energy to an existing force field, in this case CHARMM. It is demonstrated that anisotropic electrostatics reduce the RMSE for water (by 1.4 kcal/mol), CH   2 Cl   2 (by 0.8 kcal/mol) and for solvated Cl   - clusters (by 0.4 kcal/mol). An additional polarization term can be neglected for CH   2 Cl   2 but further improves the models for pure water (by ∼ 1.0 kcal/mol) and hydrated Cl   - (by 0.4 kcal/mol), and is key for solvated K   + , reducing the RMSE by 2.3 kcal/mol. A 12-6 Lennard-Jones functional form performs satisfactorily with PC and MDCM electrostatics, but is not appropriate for descriptions that account for the electrostatic penetration energy. The importance of many-body contributions is assessed by comparing a strictly 2-body approach with self-consistent reference data. Two-body interactions suffice for CH   2 Cl   2 whereas water and solvated K   + and Cl   - ions require explicit many-body corrections. Finally, a many-body-corrected dimer potential energy surface exceeds the accuracy attained using a conventional empirical force field, potentially reaching that of an FMO calculation. The present work systematically quantifies which terms improve the performance of an existing force field and what reference data to use for parametrizing these terms in a tractable fashion for ML fitting of pure and heterogeneous systems., (© 2024 The Authors. Journal of Computational Chemistry published by Wiley Periodicals LLC.)

The dynamics of lysozyme is probed by attaching -SCN to all alanine residues. The one-dimensional infrared spectra exhibit frequency shifts in the position of the maximum absorption of 4 cm-1, which is consistent with experiments in different solvents and indicates moderately strong interactions of the vibrational probe with its environment. Isotopic substitution 12C → 13C leads to a redshift by -47 cm-1, which agrees quantitatively with experiments for CN-substituted copper complexes in solution. The low-frequency, far-infrared part of the protein spectra contains label-specific information in the difference spectra when compared with the wild type protein. Depending on the position of the labels, local structural changes are observed. For example, introducing the -SCN label at Ala129 leads to breaking of the α-helical structure with concomitant change in the far-infrared spectrum. Finally, changes in the local hydration of SCN-labeled alanine residues as a function of time can be related to the reorientation of the label. It is concluded that -SCN is potentially useful for probing protein dynamics, both in the high-frequency part (CN-stretch) and in the far-infrared part of the spectrum., (© 2024 Author(s). Published under an exclusive license by AIP Publishing.)

The reaction dynamics of H 2 COO to form HCOOH and dioxirane as first steps for OH-elimination is quantitatively investigated. Using a machine learned potential energy surface (PES) at the CASPT2/aug-cc-pVTZ level of theory vibrational excitation along the CH-normal mode ν CH with energies up to 40.0 kcal mol -1 (∼5 ν CH ) leads almost exclusively to HCOOH which further decomposes into OH + HCO. Although the barrier to form dioxirane is only 21.4 kcal mol -1 the reaction probability to form dioxirane is two orders of magnitude lower if the CH-stretch mode is excited. Following the dioxirane-formation pathway is facile, however, if the COO-bend vibration is excited together with energies equivalent to ∼2 ν CH or ∼3 ν COO . For OH-formation in the atmosphere the pathway through HCOOH is probably most relevant because the alternative pathways (through dioxirane or formic acid) involve several intermediates that can de-excite through collisions, relax via internal vibrational relaxation (IVR), or pass through loose and vulnerable transition states (formic acid). This work demonstrates how, by selectively exciting particular vibrational modes, it is possible to dial into desired reaction channels with a high degree of specificity.

The role of numerical accuracy in training and evaluating neural network-based potential energy surfaces is examined for different experimental observables. For observables that require third- and fourth-order derivatives of the potential energy with respect to Cartesian coordinates single-precision arithmetics as is typically used in ML-based approaches is insufficient and leads to roughness of the underlying PES as is explicitly demonstrated. Increasing the numerical accuracy to double-precision gives a smooth PES with higher-order derivatives that are numerically stable and yield meaningful anharmonic frequencies and tunneling splitting as is demonstrated for H 2 CO and malonaldehyde. For molecular dynamics simulations, which only require first-order derivatives, single-precision arithmetics appears to be sufficient, though.

The structure and dynamics of a molecular system is governed by its potential energy surface (PES), representing the total energy as a function of the nuclear coordinates. Obtaining accurate potential energy surfaces is limited by the exponential scaling of Hilbert space, restricting quantitative predictions of experimental observables from first principles to small molecules with just a few electrons. Here, we present an explicitly physics-informed approach for improving and assessing the quality of families of PESs by modifying them through linear coordinate transformations based on experimental data. We demonstrate this "morphing" of the PES for the He - H 2 + complex using recent comprehensive Feshbach resonance (FR) measurements for reference PESs at three different levels of quantum chemistry. In all cases, the positions and intensities of peaks in the energy distributions are improved. We find these observables to be mainly sensitive to the long-range part of the PES.

The decomposition dynamics of vibrationally excited syn- CH 3 CHOO to form vinoxy + hydroxyl (CH 2 CHO + OH) radicals or to recombine to form glycolaldehyde (CH 2 OHCHO) are characterized using statistically significant numbers of molecular dynamics simulations using a full-dimensional neural-network-based potential energy surface at the CASPT2 level of theory. The computed final OH-translational and rotational state distributions agree well with experiments and probe the still unknown O-O bond strength D e OO for which best values from 22 to 25 kcal/mol are found. OH-elimination rates are consistent with experiments and do not vary appreciably with D e OO due to the non-equilibrium nature of the process. In addition to the OH-elimination pathway, OH roaming is observed following O-O scission, which leads to glycolaldehyde formation on the picosecond time scale. Together with recent work involving the methyl-ethyl-substituted Criegee intermediate, we conclude that OH roaming is a general pathway to be included in molecular-level modeling of atmospheric processes. This work demonstrates that atomistic simulations with machine-learned energy functions provide a viable route for exploring the chemistry and reaction dynamics of atmospheric reactions.

The dynamics of hyperthermal N( 4 S) + O 2 collisions were investigated both experimentally and theoretically. Crossed molecular beams experiments were performed at an average center-of-mass (c.m.) collision energy of ⟨ E coll ⟩ = 77.5 kcal mol -1 ) and reactive (NO + O) product channels were identified. In the c.m. reference frame, the nonreactively scattered N atoms and reactively scattered NO molecules were both directed into the forward direction with respect to the initial direction of the reagent N atoms. On average, more than 90% of the available energy (⟨ 2 ) and reactive (NO + O) product channels were identified. In the c.m. reference frame, the nonreactively scattered N atoms and reactively scattered NO molecules were both directed into the forward direction with respect to the initial direction of the reagent N atoms. On average, more than 90% of the available energy (⟨ E avl ⟩ = 77.5 kcal mol -1 ) was retained in translation of the nonreactive products (N + O 2 ) went into translation of the NO + O products, and the distribution of translational energies for this channel was broad, indicating extensive internal excitation in the nascent NO molecules. The experimentally derived c.m. translational energy and angular distributions of the reactive products suggested at least two dynamical pathways to the formation of NO + O. Quasiclassical trajectory (QCT) calculations were performed with a collision energy of E avl ⟩ = 109.5 kcal mol -1 ) went into translation of the NO + O products, and the distribution of translational energies for this channel was broad, indicating extensive internal excitation in the nascent NO molecules. The experimentally derived c.m. translational energy and angular distributions of the reactive products suggested at least two dynamical pathways to the formation of NO + O. Quasiclassical trajectory (QCT) calculations were performed with a collision energy of E A') surfaces. When analyzed with this theoretical insight, the experimental c.m. translational energy and angular distributions were in reasonably good agreement with those predicted by the QCT calculations, although minor differences were observed which are discussed. Theoretical translational energy and angular distributions for the nonreactive N + O coll = 77 kcal mol -1 using two sets of potential energy surfaces, denoted as PES-I and PES-II, and these theoretical results were compared to each other and to the experimental results. PES-I is a reproducing kernel Hilbert space (RKHS) representation of multireference configurational interaction (MRCI) energies, while PES-II is a many-body permutation invariant polynomial (MB-PIP) fit of complete active space second order perturbation (CASPT2) points. The theoretical investigations were both consistent with the experimental suggestion of two dynamical pathways to produce NO + O, where reactive collisions may proceed on the doublet (1 2 A') and quartet (1 4 A') surfaces. When analyzed with this theoretical insight, the experimental c.m. translational energy and angular distributions were in reasonably good agreement with those predicted by the QCT calculations, although minor differences were observed which are discussed. Theoretical translational energy and angular distributions for the nonreactive N + O 2 products matched the experimental translational energy and angular distributions almost quantitatively. Finally, relative yields for the nonreactive and reactive scattering channels were determined from the experiment and from both theoretical methods, and all results are in reasonable agreement.

Vibrational spectroscopy in supersonic jet expansions is a powerful tool to assess molecular aggregates in close to ideal conditions for the benchmarking of quantum chemical approaches. The low temperatures achieved as well as the absence of environment effects allow for a direct comparison between computed and experimental spectra. This provides potential benchmarking data which can be revisited to hone different computational techniques, and it allows for the critical analysis of procedures under the setting of a blind challenge. In the latter case, the final result is unknown to modellers, providing an unbiased testing opportunity for quantum chemical models. In this work, we present the spectroscopic and computational results for the first HyDRA blind challenge. The latter deals with the prediction of water donor stretching vibrations in monohydrates of organic molecules. This edition features a test set of 10 systems. Experimental water donor OH vibrational wavenumbers for the vacuum-isolated monohydrates of formaldehyde, tetrahydrofuran, pyridine, tetrahydrothiophene, trifluoroethanol, methyl lactate, dimethylimidazolidinone, cyclooctanone, trifluoroacetophenone and 1-phenylcyclohexane- cis -1,2-diol are provided. The results of the challenge show promising predictive properties in both purely quantum mechanical approaches as well as regression and other machine learning strategies.

Full-dimensional potential energy surfaces (PESs) based on machine learning (ML) techniques provide a means for accurate and efficient molecular simulations in the gas and condensed phase for various experimental observables ranging from spectroscopy to reaction dynamics. Here, the MLpot extension with PhysNet as the ML-based model for a PES is introduced into the newly developed pyCHARMM application programming interface. To illustrate the conception, validation, refining, and use of a typical workflow, para-chloro-phenol is considered as an example. The main focus is on how to approach a concrete problem from a practical perspective and applications to spectroscopic observables and the free energy for the -OH torsion in solution are discussed in detail. For the computed IR spectra in the fingerprint region, the computations for para-chloro-phenol in water are in good qualitative agreement with experiment carried out in CCl4. Moreover, relative intensities are largely consistent with experimental findings. The barrier for rotation of the -OH group increases from ∼3.5 kcal/mol in the gas phase to ∼4.1 kcal/mol from simulations in water due to favorable H-bonding interactions of the -OH group with surrounding water molecules., (© 2023 Author(s). Published under an exclusive license by AIP Publishing.)