A new ab initio potential energy surface for the NeCO complex with the vibrational coordinate dependence.
Ontology highlight
ABSTRACT:
SUBMITTER: Wang Z
PROVIDER: S-EPMC3036545 | biostudies-other | 2011 Jan
REPOSITORIES: biostudies-other
Similar Datasets
Project description:We built a full-dimensional analytical potential energy surface of the ground electronic state of Li₂H from ca. 20,000 ab initio multi-reference configuration interaction calculations, including core⁻valence correlation effects. The surface is flexible enough to accurately describe the three dissociation channels: Li (2s ²S) + LiH (¹Σ⁺), Li₂ (¹Σg⁺) + H (1s ²S) and 2Li (2s ²S) + H (1s ²S). Using a local fit of this surface, we calculated pure (J = 0) vibrational states of Li₂H up to the barrier to linearity (ca. 3400 cm-1 above the global minimum) using a vibrational self-consistent field/virtual state configuration interaction method. We found 18 vibrational states below this barrier, with a maximum of 6 quanta in the bending mode, which indicates that Li₂H could be spectroscopically observable. Moreover, we show that some of these vibrational states are highly correlated already ca. 1000 cm-1 below the height of the barrier. We hope these calculations can help the assignment of experimental spectra. In addition, the first low-lying excited states of each B₁, B₂ and A₂ symmetry of Li₂H were characterized.
| S-EPMC6337435 | biostudies-literature
Project description:The potential energy surface and vibration-rotation energy levels of aluminum monohydroxide in the X̃ 1A' electronic state have been determined from ab initio calculations. The equilibrium configuration of the AlOH molecule was found to be bent, although with a wide AlOH angle of 163° and a small barrier to linearity of just 4 cm-1. The AlOH molecule was definitely confirmed to be quasilinear. The predicted spectroscopic constants of the AlOH, AlOD, 26AlOH, and Al18OH isotopologues can be useful in a future analysis of high-resolution vibration-rotation spectra of these species.
| S-EPMC10591505 | biostudies-literature
Project description:Ab initio molecular dynamics simulations (AIMD) are systematically performed to study the Vibrational Energy Redistribution (VER) in solid nitromethane (NM) by combining normal mode decomposition and short-time Fourier transform technique. After the selective excitations of all fourteen intramolecular vibrational modes above 400 cm-1, four three-dimensional (3D) excitation and detected vibrational spectra are obtained. The evolution of the kinetic energy proportion of all vibrations are also given and discussed quantitatively. These results show that, as the daughter modes, NO2 symmetric stretches, CH3 stretches and bends are usually excited quickly and relatively conspicuously compared with the other vibrations. Interestingly, we found that, although the stretching vibration of the CN bond which is a bridge between the methyl and nitro group can not respond immediately to the selective excitations, it always accumulates the vibrational energy slowly and steadily. Then, the underlying mechanisms are discussed based on the response of vibrational modes in both the time and frequency domain. As a result, we found that anharmonic transfers following symmetry rules which involve the couplings assisted by the overtones and rotations, as well as the transfers among the adjacent modes, play important roles in the VER of solid NM.
| S-EPMC8695419 | biostudies-literature
Project description:The rates of intramolecular proton transfer are calculated on a full-dimensional reactive electronic potential energy surface that incorporates high level ab initio calculations along the reaction path and by using classical Transition State theory, Path-Integral Quantum Transition State Theory, and the Quantum Instanton approach. The specific example problem studied is malonaldehyde. Estimates of the kinetic isotope effect using the latter two methods are found to be in reasonable agreement with each other. Improvements and extensions of this practical, yet chemically accurate framework for the calculations of quantized, reactive dynamics are also discussed.
| S-EPMC2992356 | biostudies-literature
Project description:We present an on-the-fly ab initio semiclassical study of vibrational energy levels of glycine, calculated by Fourier transform of the wavepacket correlation function. It is based on a multiple coherent states approach integrated with monodromy matrix regularization for chaotic dynamics. All four lowest-energy glycine conformers are investigated by means of single-trajectory semiclassical spectra obtained upon classical evolution of on-the-fly trajectories with harmonic zero-point energy. For the most stable conformer I, direct dynamics trajectories are also run for each vibrational mode with energy equal to the first harmonic excitation. An analysis of trajectories evolved up to 50 000 atomic time units demonstrates that, in this time span, conformers II and III can be considered as isolated species, while conformers I and IV show a pretty facile interconversion. Therefore, previous perturbative studies based on the assumption of isolated conformers are often reliable but might be not completely appropriate in the case of conformer IV and conformer I for which interconversion occurs promptly.
| S-EPMC5472367 | biostudies-literature
Project description:We construct a full-dimensional ab initio neural network potential energy surface (PES) for the isomerization system of the formic acid dimer (FAD). This is based upon ab initio calculations using the DLPNO-CCSD(T) approach with the aug-cc-pVTZ basis set, performed at over 14000 symmetry-unique geometries. An accurate fit to the obtained energies is generated using a general neural network fitting procedure combined with the fundamental invariant method, and the overall energy-weighted root-mean-square fitting error is about 6.4 cm-1. Using this PES, we present a multidimensional quantum dynamics study on tunneling splittings with an efficient theoretical scheme developed by our group. The ground-state tunneling splitting of FAD calculated with a four-mode coupled method is in good agreement with the most recent experimental measurements. The PES can be applied for further dynamics studies. The effectiveness of the present scheme for constructing a high-dimensional PES is demonstrated, and this scheme is expected to be feasible for larger molecular systems.
| S-EPMC10193396 | biostudies-literature
Project description:The routine prediction of three-dimensional protein structure from sequence remains a challenge in computational biochemistry. It has been intuited that calculated energies from physics-based scoring functions are able to distinguish native from nonnative folds based on previous performance with small proteins and that conformational sampling is the fundamental bottleneck to successful folding. We demonstrate that as protein size increases, errors in the computed energies become a significant problem. We show, by using error probability density functions, that physics-based scores contain significant systematic and random errors relative to accurate reference energies. These errors propagate throughout an entire protein and distort its energy landscape to such an extent that modern scoring functions should have little chance of success in finding the free energy minima of large proteins. Nonetheless, by understanding errors in physics-based score functions, they can be reduced in a post-hoc manner, improving accuracy in energy computation and fold discrimination.
| S-EPMC3081830 | biostudies-literature
Project description:The advent of machine learning potentials (MLPs) provides a unique opportunity to access simulation time scales and to directly compute physicochemical properties that are typically intractable using density functional theory (DFT). In this study, we use an active learning curriculum to train a generalizable MLP using the DeepMD-kit architecture. By using sufficiently long MLP-based molecular dynamics (MD) simulations, which provide DFT-level accuracy, we investigate the diffusion of key surface-bound adsorbates on a Ag(111) facet. Detailed analysis of the MLP/MD-calculated diffusivities sheds light on the potential shortcomings of using DFT-based nudged elastic band to estimate surface diffusion barriers. More generally, while this study is focused on a specific system, we anticipate that the underlying workflows and the resulting models can be extended to other adsorbates and other materials in the future.
| S-EPMC11317978 | biostudies-literature
Project description:The interplay between light absorption and the molecular environment has a central role in the observed photophysics of a wide range of photoinduced chemical and biological phenomena. The understanding of the interplay between vibrational and electronic transitions is the focus of this work, since it can provide a rationale to tune the optical properties of charge transfer (CT) materials used for technological applications. A clear description of these processes poses a nontrivial challenge from both the theoretical and experimental points of view, where the main issue is how to accurately describe and probe drastic changes in the electronic structure and the ultrafast molecular relaxation and dynamics. In this work we focused on the intermolecular CT reaction that occurs upon photon absorption in a π-stacked model system in dichloromethane solution, in which the 1-chloronaphthalene (1ClN) acts as the electron donor and tetracyanoethylene (TCNE) is the electron acceptor. Density functional theory calculations have been carried out to characterize both the ground-state properties and more importantly the low-lying CT electronic transition, and excellent agreement with recently available experimental results [Mathies, R. A.; et al. J. Phys. Chem. A 2018, 122 (14), 3594] was obtained. The minima of the ground state and first singlet excited state have been accurately characterized in terms of spatial arrangements and vibrational Raman frequencies, and the CT natures of the first two low-lying electronic transitions in the absorption spectra have been addressed and clarified too. Finally, by modeling the possible coordination sites of the TCNE electron acceptor with respect to monovalent ions (Na+, K+) in an implicit solution of acetonitrile, we find that TCNE can accommodate a counterion in two different arrangements, parallel and orthogonal to the C═C axis, leading to the formation of a contact ion pair. The nature of the counterion and its relative position entail structural modifications of the TCNE radical anion, mainly the central C═C and C≡N bonds, compared to the isolated case. An important red shift of the C═C stretching frequency was observed when the counterion is orthogonal to the double bond, to a greater extent for Na+. On the contrary, in the second case, where the counterion ion lies along the internuclear C═C axis, we find that K+ polarizes the electron density of the double bond more, resulting in a greater red shift than with Na+.
| S-EPMC9574931 | biostudies-literature
Project description:Accurate prediction of the placement and comformations of protein side chains given only the backbone trace has a wide range of uses in protein design, structure prediction, and functional analysis. Prediction has most often relied on discrete rotamer libraries so that rapid fitness of side-chain rotamers can be assessed against some scoring function. Scoring functions are generally based on experimental parameters from small-molecule studies or empirical parameters based on determined protein structures. Here, we describe the NCN algorithm for predicting the placement of side chains. A predominantly first-principles approach was taken to develop the potential energy function incorporating van der Waals and electrostatics based on the OPLS parameters, and a hydrogen bonding term. The only empirical knowledge used is the frequency of rotameric states from the PDB. The rotamer library includes nearly 50,000 rotamers, and is the most extensive discrete library used to date. Although the computational time tends to be longer than most other algorithms, the overall accuracy exceeds all algorithms in the literature when placing rotamers on an accurate backbone trace. Considering only the most buried residues, 80% of the total residues tested, the placement accuracy reaches 92% for chi(1), and 83% for chi(1 + 2), and an overall RMS deviation of 1 A. Additionally, we show that if information is available to restrict chi(1) to one rotamer well, then this algorithm can generate structures with an average RMS deviation of 1.0 A for all heavy side-chains atoms and a corresponding overall chi(1 + 2) accuracy of 85.0%.
| S-EPMC2286725 | biostudies-literature