Zero-point Vibrational Energy Research Articles

Quantum chemical pathways for the formation of 2,3,7,8-tetrachloro dibenzo-p-dioxin (TCDD) from 2,4,5-trichlorophenol: a mechanistic and thermo-kinetic study.

Dioxins, specifically 2,3,7,8-tetrachlorinated dibenzo-p-dioxin (TCDD), are highly toxic dioxins known for their severe health impacts and persistent environmental pollutants. This study focuses on understanding the formation pathways of TCDD from its precursor molecule 2,4,5-trichlorophenol (2,4,5-TCP). In our exploration of reaction pathways from 2,4,5-trichlorophenol (TCP), we delve into three reaction mechanisms: free-radical, direct condensation, and anionic. Our findings highlight the significance of the radical mechanism, particularly propagated by H radicals, with a notable increase in dioxin formation around 900K. These results are consistent with experimental observations indicating an increase in the conversion of trichlorophenol from 600 to 900K in the non-catalytic gas phase reaction. Thermodynamic parameters (∆H, ∆S, and ∆G), reaction barriers, and rate constants (k) were calculated across a temperature range of 300-1200K to support the findings and provide insights into the optimal temperature range for controlling dioxins during the incineration process. In this study, quantum chemical calculations were conducted using density functional theory (DFT) with the B3LYP functional and the 6-311 + + G(d,p) basis set in Gaussian 16 software. Stationary points, including transition states (TS), were confirmed with frequency calculations. Intrinsic reaction coordinate (IRC) calculations ensured minimum energy paths between TS and products, visualized in GaussView 6.0 Program. Single-point energy calculations utilized a more precise basis set, 6-311 + + G(3df,2p), for enhanced energy accuracy, incorporating zero-point vibrational energy (ZPE) and other energy corrections. These calculations were repeated over a temperature range of 298.15-1200K at 1atm pressure. Finally, rate constant (k) expressions associated with TCDD formation were determined using transition state theory (TST).

Quantum Monte Carlo Simulations of the Vibrational Wavefunction of the Aromatic Cyclo[10]carbon Using a Full Dimensional Permutationally Invariant Potential Energy Surface.

New experimental measurements [Sun et al., Nature 2023, 623, 972] of the cyclic C10 reveal a cumulenic pentagon-like D5h structure at ∼5 K. However, the long-standing presumption that a large zero-point vibrational energy combined with an extremely flat D5h ↔ D10h ↔ D5h isomerization pathway washes out the pentagonal D5h structure and yields a symmetric D10h decagon remains at odds with the experiment. We resolve this issue with our fitting approach based on a bond-order charge-density matrix expressed in permutationally invariant polynomials. We train the model on τHCTH/cc-pVQZ data morphed to reproduce a relativistic all-electron CCSDT(Q)/CBS D5h-D10h potential energy barrier (benchmarked previously by others). Large scale diffusion Monte Carlo simulations in full dimensionality show that the vibrational ground state of C10 has compositional character of more than 96% D5h, fully reflecting the experimental imaging data. Quantum mechanical variational calculations in 1-D further suggest persistence of the D5h symmetry structure at higher temperatures.

Anharmonic rotational and vibrational spectroscopic constants of NH2CH2OH

The recent experimental identification of aminomethanol (NH2CH2OH) and its synthesis under simulated interstellar conditions suggests that it may be formed, and thus observable, in the interstellar medium. To aid in its possible detection, this work presents high-level theoretical, anharmonic vibrational and rotational spectroscopic data for the three lowest-energy conformers of NH2CH2OH. All three conformers fall within 0.80 kcal mol−1 of each other at the CCSD(T)-F12b/cc-pCVTZ-F12 level, with an anharmonic zero-point vibrational energy correction. Additionally, all three conformers are shown to have multiple vibrational frequencies with intensities greater than 100 km mol−1. The most notable of these are the symmetric O-C-N stretch of the lower-energy C1 conformer at 976.4 cm−1, the C-O stretch of the Cs conformer at 964.9 cm−1, and the antisymmetric O-C-N stretch of the higher-energy C1 conformer at 1099.0 cm−1. While much of the vibrational spectra of the three overlap, these features should help to separate them. Finally, all three conformers have non-zero dipole moments on the order of 1 D, suggesting that they may be observable by rotational spectroscopy, as well. In all cases, the computational data provided herein will help to facilitate future experimental and observational studies on this key molecule in the formation of extraterrestrial amino acids.

DFT and TD-DFT studies of perovskite materials LiAX3 (A=Ge, Sn; X= F, Cl, Br, I) in reference to their solar cell applications

Halide perovskite materials have attracted a huge interest of researchers due to their fascinating optoelectronic properties. In this report, structural, electronic, optical, and thermoelectric properties of Li-based perovskite materials LiAX3 (A = Ge, Sn; X = F, Cl, Br, I) are analyzed using Density Functional Theory (DFT). Functionals- B3LYP/LanL2DZ, B3LYP/def2-TZVP and B3LYP/LanL08 within the DFT framework are applied for geometry optimization of these perovskites. The results show a marked variation in magnitude of HOMO-LUMO energy gap of LiGeX3 and LiSnX3 with respect to different functionals viz. B3LYP/LanL2DZ, B3LYP/def2-TZVP and B3LYP/LanL08. LiGeF3 and LiSnF3 show the maximum values of HOMO-LUMO energy gap. The computed energy gap lies in the range required for perovskite materials to exhibit solar cell applications. A number of CDFT-based descriptors and Optical properties of LiAX3 are also studied and reported accordingly. Our computed results show that lattice constants, volume, formation energy, polarizability, refractive index, dielectric constant, entropy, heat capacity and wavelength of LiAX3 increases from F to I, whereas, HOMO-LUMO energy gap, electronegativity, electrophilicity index, optical electronegativity, vibrational frequencies, peak IR intensity, vibrational energy, total energy, zero-point vibrational energy, Gibbs free energy and photon energy decreases in the reverse direction.

Tell Machine Learning Potentials What They Are Needed For: Simulation-Oriented Training Exemplified for Glycine.

Machine learning potentials (MLPs) are widely applied as an efficient alternative way to represent potential energy surfaces (PESs) in many chemical simulations. The MLPs are often evaluated with the root-mean-square errors on the test set drawn from the same distribution as the training data. Here, we systematically investigate the relationship between such test errors and the simulation accuracy with MLPs on an example of a full-dimensional, global PES for the glycine amino acid. Our results show that the errors in the test set do not unambiguously reflect the MLP performance in different simulation tasks, such as relative conformer energies, barriers, vibrational levels, and zero-point vibrational energies. We also offer an easily accessible solution for improving the MLP quality in a simulation-oriented manner, yielding the most precise relative conformer energies and barriers. This solution also passed the stringent test by diffusion Monte Carlo simulations.

Convergent abinitio analysis of the multi-channel HOBr + H reaction.

High-level potential energy surfaces for three reactions of hypobromous acid with atomic hydrogen were computed at the CCSDTQ/CBS//CCSDT(Q)/complete basis set level of theory. Focal point analysis was utilized to extrapolate energies and gradients for energetics and optimizations, respectively. The H attack at Br and subsequent Br-O cleavage were found to proceed barrierlessly. The slightly submerged transition state lies -0.2kcal mol-1 lower in energy than the reactants and produces OH and HBr. The two other studied reaction paths are the radical substitution to produce H2O and Br with a 4.0kcal mol-1 barrier and the abstraction at hydrogen to produce BrO and H2 with an 11.2kcal mol-1 barrier. The final product energies lie -37.2, -67.9, and -7.3kcal mol-1 lower in energy than reactants, HOBr + H, for the sets of products OH + HBr, H2O + Br, and H2 + BrO, respectively. Additive corrections computed for the final energetics, particularly the zero-point vibrational energies and spin-orbit corrections, significantly impacted the final stationary point energies, with corrections up to 6.2kcal mol-1.

Study on the Mechanism of Lipid Peroxidation Induced by Carbonate Radicals.

Based on the reported research, hydroxyl radicals can be rapidly transformed into carbonate radicals in the carbonate-bicarbonate buffering system in vivo. Many of the processes considered to be initiated by hydroxyl radicals may be caused by carbonate radicals, which indicates that lipid peroxidation initiated by hydroxyl radicals can also be caused by carbonate radicals. To date, theoretical research on reactions of hydrogen abstraction from and radical addition to polyunsaturated fatty acids (PUFAs) of carbonate radicals has not been carried out systematically. This paper employs (3Z,6Z)-nona-3,6-diene (NDE) as a model for polyunsaturated fatty acids (PUFAs). Density functional theory (DFT) with the CAM-B3LYP method at the 6-311+g(d,p) level was used to calculate the differences in reactivity of carbonate radicals abstracting hydrogen from different positions of NDE and their addition to the double bonds of NDE under lipid solvent conditions with a dielectric constant of 4.0 (CPCM model). Grimme's empirical dispersion correction was taken into account through the D3 scheme. The energy barrier, reaction rate constants, internal energy, enthalpy and Gibbs free energy changes in these reactions were calculated With zero-point vibrational energy (ZPVE) corrections. The results indicated that carbonate radicals initiate lipid peroxidation primarily through hydrogen abstraction from diallyl carbon atoms. The reaction of hydrogen abstraction from diallyl carbon atoms exhibits the highest reaction rate, with a reaction rate constant approximately 43-fold greater than the second-ranked hydrogen abstraction from allyl carbon atoms. This process has the lowest energy barrier, internal energy, enthalpy, and Gibbs free energy changes, indicating that it is also the most spontaneous process.

Efficient interpolation of molecular properties across chemical compound space with low-dimensional descriptors

We demonstrate accurate data-starved models of molecular properties for interpolation in chemical compound spaces with low-dimensional descriptors. Our starting point is based on three-dimensional, universal, physical descriptors derived from the properties of the distributions of the eigenvalues of Coulomb matrices. To account for the shape and composition of molecules, we combine these descriptors with six-dimensional features informed by the Gershgorin circle theorem. We use the nine-dimensional descriptors thus obtained for Gaussian process regression based on kernels with variable functional form, leading to extremely efficient, low-dimensional interpolation models. The resulting models trained with 100 molecules are able to predict the product of entropy and temperature (S × T) and zero point vibrational energy (ZPVE) with the absolute error under 1 kcal mol−1 for >78 % and under 1.3 kcal mol−1 for >92 % of molecules in the test data. The test data comprises 20 000 molecules with complexity varying from three atoms to 29 atoms and the ranges of S × T and ZPVE covering 36 kcal mol−1 and 161 kcal mol−1, respectively. We also illustrate that the descriptors based on the Gershgorin circle theorem yield more accurate models of molecular entropy than those based on graph neural networks that explicitly account for the atomic connectivity of molecules.

Energetic and Spectroscopic Properties of Astrophysically Relevant MgC4H Radicals Using High-Level Ab Initio Calculations.

Considering the importance of magnesium-bearing hydrocarbon molecules (MgCnH; n = 2, 4, and 6) in the carbon-rich circumstellar envelopes (e.g., IRC+10216), a total of 28 constitutional isomers of MgC4H have been theoretically investigated using density functional theory (DFT) and coupled-cluster methods. The zero-point vibrational energy corrected relative energies at the ROCCSD(T)/cc-pCVTZ level of theory reveal that the linear isomer, 1-magnesapent-2,4-diyn-1-yl (1, 2Σ+), is the global minimum geometry on the MgC4H potential energy surface. The latter has been detected both in the laboratory and in the evolved carbon star, IRC+10216. The calculated spectroscopic data for 1 match well with the experimental observations (error ∼ 0.78%) which validates our theoretical methodology. Plausible isomerization processes happening among different isomers are examined using DFT and coupled-cluster methods. CASPT2 calculations have been performed for a few isomers exhibiting multireference characteristics. The second most stable isomer, 1-ethynyl-1λ3-magnesacycloprop-2-ene-2,3-diyl (2, 2A1, μ = 2.54 D), is 146 kJ mol-1 higher in energy than 1 and possibly the next promising candidate to be detected in the laboratory or in the interstellar medium in future.

Exploring the Tl H potential energy surface: A comparative analysis with group 13 systems and experiment.

Thallium chemistry is experiencing unprecedented importance. Therefore, it is valuable to characterize some of the simplest thallium compounds. Stationary points along the singlet and triplet Tl H potential energy surface have been characterized. Stationary point geometries were optimized with the CCSD(T)/aug-cc-pwCVQZ-PP method. Harmonic vibrational frequencies were computed at the same level of theory while anharmonic vibrational frequencies were computed at the CCSD(T)/aug-cc-pwCVTZ-PP level of theory. Final energetics were obtained with the CCSDT(Q) method. Basis sets up to augmented quintuple-zeta cardinality (aug-cc-pwCV5Z-PP) were employed to obtain energetics in order to extrapolate to the complete basis set limits using the focal point approach. Zero-point vibrational energy corrections were appended to the extrapolated energies in order to determine relative energies at 0 K. It was found that the planar dibridged isomer lies lowest in energy while the linear structure lies highest in energy. The results were compared to other group 13 M H (M = B, Al, Ga, In, and Tl) theoretical studies and some interesting variations are found. With respect to experiment, incompatibilities exist.

A wealth of structures for the Ge2H2+ radical cation: comparison of theory and experiment.

Five structures of Ge2H2 and Ge2H2+ are investigated in this study. Optimized geometries at the CCSD(T)/cc-pwCVQZ-PP level of theory were obtained. Focal point analyses were performed on these optimized geometries to determine relative energies using the CCSD(T) method with polarized basis sets up to quintuple-zeta. Energy corrections include full T and pertubative (Q) coupled-cluster effects plus anharmonic corrections to the zero-point vibrational energy. Relative ordering in energy from lowest to highest of the five Ge2H2+ structures is butterfly, germylidene, monobridged, trans, then linear. In neutral Ge2H2, the monobridged structure lies lower in energy than the germylidene structure. Fundamental vibrational frequencies and IR intensities were computed for the minima at the CCSD(T)/cc-pwCVTZ-PP level of theory to compare with experimental research. Partial atomic charges and natural bonding orbital analyses indicated that the positive charge of Ge2H2+ is contained in the region of the Ge-Ge bond.

The heavy Carbene analogues SbH2 + and BiH2 +. Convergent quantum mechanical studies*

In 2021 Olaru, Mebs, and Beckmann reported the synthesis of remarkable cationic carbene analogues P R 2 + and As R 2 + . This work followed the same group's synthesis of Sb R 2 + and Bi R 2 + . To better understand these important systems, Sb H 2 + and Bi H 2 + have been studied with high level ab initio quantum mechanical methods. Geometries were optimised with the CCSDT(Q) method with the cc-pwCVTZ-PP basis set using small core pseudopotentials. Fundamental vibrational frequencies were computed to provide theoretical predictions for future synthetic studies. Relative energies with respect to P n + + H 2 ( Pn = Sb , Bi ) were determined at the CCSDT/CBS level of theory via the Focal Point Analysis method, and anharmonic zero-point vibrational energy and higher order contributions were also computed. For Sb H 2 + , we obtained R = 1.697 Å and θ = 90.8 ∘ with S b + + H 2 → Sb H 2 + reaction enthalpy of ΔH = − 18.71 kcal mol − 1 . For Bi H 2 + , the analogous results were R = 1.774 Å, θ = 89.7 ∘ , and ΔH = − 7.64 kcal mol − 1 for B i + + H 2 → Bi H 2 + .

Simulation of dissociation effect at high temperature and high pressure by REMC method

Considering the zero-point vibration energy of fluid H2, the dissociation process of fluid H2 at different temperatures and densities under 10000 K was studied by using the REMC (reaction ensemble Monte Carlo) method based on classical theory, and the results of different methods were compared and analyzed. The variation of the dissociation degree with temperature predicted by the REMC method is similar to that of the DM method, and the value of the dissociation degree is closest to that of the TB-II method. The dissociation degree of fluid H2 is less than 38% at 10000 K. According to this REMC method, the fluid D2 begins to dissociate when the shock pressure reaches 20 GPa. When the shock pressure is 50 GPa, the dissociation degree is 23.88%; At 100 GPa, the dissociation degree is 61.30%. The calculated dissociation value of fluid D2 is lower than that of the QMD method under high temperature and high pressure, while it is in good agreement with the experimental results derived from light gas gun under low temperature and low pressure.

Quantum Chemical Studies on Structural, Spectral and Frontier Molecular Orbital Analysis of Indometacin in Aqueous Phases

Density functional theory computations were done by using 6-31G(d) basis set in order to check out the solubility of indometacin in polar and non-polar solvents such as water, ethanol, acetone and diethyl ether, respectively. The quantum chemical parameters of indometacin in gaseous as well as in aqueous phases were calculated. The most stable structure (indometacin in water; IM-W) was found to be more stable with respect to the least stable complex (indometacin in diethyl ether; IM-D) by 3.14 Kcal/mol. The zero-point vibrational energy of indometacin in gas phase was found to be 197.731 Kcal/mol. The fundamental vibrational modes of indometacin were assignment and analyzed at B3LYP/6-31G(d) level of theory. The HOMO–LUMO analysis of indometacin showed that its HOMO is concentrated at its indole ring and LUMO is at its chlorophenyl group. The charge density distribution of indometacin was investigated through the molecular electrostatic potential map.

The zero-point vibration contributions to energy and compressibility of light rare-gas solids

The zero-point vibration energy, Gruneisen coefficient, and zero-point vibration pressure of light rare-gas solids (LRGS)(He, Ne, Ar) are calculated within a certain range of atomic spacing using many-body expansion and ab initio calculation methods based on quantum and atomic cluster theories. The results are then compared with the previous theoretical calculations and experimental data. It is concluded that the smaller the molar volume of LRGS, the greater the crystal's zero-point vibration energy and vibration frequency. The zero-point vibration energy of LRGSis only 6% of the total many-body interaction energy but should not be neglected. The Grüneisen coefficient of LRGS increases as the molar volume increases. The zero-point vibration pressure is smaller, which is about 3% of the total pressure. The error caused by the pressure calculation is not significant, but when the molar volume is reduced to a fixed value, the zero-point vibration pressure must be considered and cannot be ignored. In addition, the calculation results of zero-point vibration pressure are compared to the previous theoretical calculations and experimental results.

Molecular structure, spectral analysis and chemical activity of sabizabulin: A computational study

In this study, a detailed computational spectroscopic investigation of sabizabulin, a small molecule known as a tubulin inhibitor with potential antineoplastic, antiviral, and anti-inflammatory activities, has been presented. Our work utilizes Density Functional Theory (DFT) calculations to explore molecular optimization, thermodynamic characteristics, and the analysis of normal modes with vibrational assignments. We calculate essential properties such as standard zero-point vibrational energy, entropy, dipole moment, etc., based on data extracted from the optimized molecular structure. Additionally, we examine Mulliken charges and the Molecular Electrostatic Potential (MEP) plot to comprehend the electronic distribution and chemical activity of sabizabulin. Our findings provide valuable insights into the spectroscopic properties of sabizabulin, highlighting its potential therapeutic applications. Our work aims to explore future research directions that could expand the understanding of sabizabulin's actions and enhance its applicability in medical treatments.

Effects of Hydrogen/Deuterium Exchange on Protein Stability in Solution and in the Gas Phase.

Mass spectrometry (MS)-based techniques are widely used for probing protein structure and dynamics in solution. H/D exchange (HDX)-MS is one of the most common approaches in this context. HDX is often considered to be a "benign" labeling method, in that it does not perturb protein behavior in solution. However, several studies have reported that D2O pushes unfolding equilibria toward the native state. The origin, and even the existence of this protein stabilization remain controversial. Here we conducted thermal unfolding assays in solution to confirm that deuterated proteins in D2O are more stable, with 2-4 K higher melting temperatures than unlabeled proteins in H2O. Previous studies tentatively attributed this phenomenon to strengthened H-bonds after deuteration, an effect that may arise from the lower zero-point vibrational energy of the deuterated species. Specifically, it was proposed that strengthened water-water bonds (W···W) in D2O lower the solubility of nonpolar side chains. The current work takes a broader view by noting that protein stability in solution also depends on water-protein (W···P) and protein-protein (P···P) H-bonds. To help unravel these contributions, we performed collision-induced unfolding (CIU) experiments on gaseous proteins generated by native electrospray ionization. CIU profiles of deuterated and unlabeled proteins were indistinguishable, implying that P···P contacts are insensitive to deuteration. Thus, protein stabilization in D2O is attributable to solvent effects, rather than alterations of intraprotein H-bonds. Strengthening of W···W contacts represents one possible explanation, but the stabilizing effect of D2O can also originate from weakened W···P bonds. Future work will be required to elucidate which of these two scenarios is correct, or if both contribute to protein stabilization in D2O. In any case, the often-repeated adage that "D-bonds are more stable than H-bonds" does not apply to intramolecular contacts in native proteins.

Structural, Spectroscopic, Mechanical, and Nonlinear Optical Properties of 4-Dimethylaminopyridinium Picrate Single Crystal for Optoelectronic Applications

A novel organic nonlinear optical (NLO) material, 4-dimethylaminopyridinium picrate (4DMAPP) with molecular formula (C7H11N2)+.(C6H2N3O7)- has been synthesized. The single crystals have been grown from synthesized material by slow evaporation technique. The NLO behavior of the 4DMAPP has been investigated using the quantum chemical calculations with 6-311++G(d,p) basis set. The bond lengths, bond angles, and torsional angle of optimized structure of 4DMAPP are in good agreement with the X-ray diffraction experimental data. The global softness, electron affinity, global hardness, Ionization potential, electronegativity, global electrophilicity, and chemical potential have been estimated. The Meyer index is found to be 2.51 and the nature of the 4DMAPP NLO material is identified as soft. Thermodynamics and molecular parameters of 4DMAPP have been carried out with zero-point vibrational energy 186.191 and 171.908 kcal/mol using Hartree–Fock (HF) and density functional theory (DFT) methods, respectively. In optical absorption spectrum, the material 4DMAPP shows the lower cut off wavelength of 325 nm. The narrow energy gap between highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) facilitates the intramolecular charge transfer (ICT) which makes the material to be NLO active.

Analytical harmonic vibrational frequencies with VV10-containing density functionals: Theory, efficient implementation, and benchmark assessments.

VV10 is a powerful nonlocal density functional for long-range correlation that is used to include dispersion effects in many modern density functionals, such as the meta-generalized gradient approximation (mGGA), B97M-V, the hybrid GGA, ωB97X-V, and the hybrid mGGA, ωB97M-V. While energies and analytical gradients for VV10 are already widely available, this study reports the first derivation and efficient implementation of the analytical second derivatives of the VV10 energy. The additional compute cost of the VV10 contributions to analytical frequencies is shown to be small in all but the smallest basis sets for recommended grid sizes. This study also reports the assessment of VV10-containing functionals for predicting harmonic frequencies using the analytical second derivative code. The contribution of VV10 to simulating harmonic frequencies is shown to be small for small molecules but important for systems where weak interactions are important, such as water clusters. In the latter cases, B97M-V, ωB97M-V, and ωB97X-V perform very well. The convergence of frequencies with respect to the grid size and atomic orbital basis set size is studied, and recommendations are reported. Finally, scaling factors to allow comparison of scaled harmonic frequencies with experimental fundamental frequencies and to predict zero-point vibrational energy are presented for some recently developed functionals (including r2SCAN, B97M-V, ωB97X-V, M06-SX, and ωB97M-V).

Isotope Effects in the Zundel-Eigen Isomerization of H+(H2O)6.

The isomerization pathway between the energetically low-lying Zundel and Eigen isomers of the protonated water hexamer was investigated using high-level ab initio calculations including a treatment of zero-point corrections. On the basis of these calculations, the Zundel-Eigen isomerization was found to proceed through a stable intermediate isomer, which consists of a four-membered ring with two single acceptor water molecules. The inclusion of vibrational zero-point energy is shown to be important for accurately establishing the relative energies of the three relevant isomers involved in the Zundel-Eigen isomerization. Diffusion Monte Carlo calculations including anharmonic vibrational effects show that all three isomers of H+(H2O)6 and D+(D2O)6 have well-defined structures. The energetic ordering of the three isomers changes upon deuteration. The implications of these results for the vibrational spectra of H+(H2O)6 and D+(D2O)6 are also discussed.