Investigation Of Potential Energy Surface Research Articles

Investigation of Potential Energy Surfaces of Reaction Systems Containing Ethylene, Hydrogen, and Oxygen Atoms by Quantum Chemical Calculations

Investigation of Potential Energy Surfaces of Reaction Systems Containing Ethylene, Hydrogen, and Oxygen Atoms by Quantum Chemical Calculations

Intramolecular Hydrogen Bonding in Thermally Activated Delayed Fluorescence Emitters: Is There Evidence Beyond Reasonable Doubt?

Intramolecular hydrogen bonding between donor and acceptor segments in thermally activated delayed fluorescence (TADF) materials is now frequently employed to—purportedly—rigidify the structure and improve the emission performance of these materials. However, direct evidence for these intramolecular interactions is often lacking or ambiguous, leading to assertions that are largely speculative. Here we investigate a series of TADF-active materials incorporating pyridine, which bestows the potential ability to form intramolecular H-bonding interactions. Despite possible indications of H-bonding from an X-ray analysis, an array of other experimental investigations proved largely inconclusive. Instead, after examining computational potential energy surfaces of the donor–acceptor torsion angle we conclude that the pyridine group primarily alleviates steric congestion in our case, rather than enabling an H-bond interaction as elsewhere assumed. We suggest that many previously reported “H-bonding” TADF materials featuring similar chemical motifs may instead operate similarly and that investigation of potential energy surfaces should become a key feature of future studies.

Prelude to Molecular Dynamics‐II: Investigation of Potential Energy Surfaces Using Gaussian Charge Models

AbstractThe current work demonstrates the application of topography‐based Gaussian charge models (GCMs) in studying potential energy surfaces of molecular dimers of water, ammonia, acetylene and benzene in addition to water‐ammonia, water‐acetylene, ammonia‐acetylene, water‐benzene, ammonia‐benzene and acetylene‐benzene complexes. Investigations are also carried for trimer systems of water, ammonia and their mixed compositions. The predicted geometries are in good agreement with those derived from quantum mechanical (QM) calculations and the interaction energy values forecasted deviate not more than ±2 kcal/mol from respective QM counterparts.

Theoretical investigation of potential energy surface and bound states for the N2-OCS van der Waals complex.

In this work we report an ab initio intermolecular potential energy surface and theoretically spectroscopic studies for N2-OCS complex. A four-dimensional intermolecular potential energy surface (4D PES) is constructed at the level of single and double excitation coupled-cluster method with a non-iterative perturbation treatment of triple excitations [CCSD(T)] with aug-cc-pVTZ basis set supplemented with bond functions. A global minimum corresponding to a planar and nearly T-shaped structure, which has been observed experimentally, is located at R = 3.96 Å, θ1 = 8 or 172°, θ2 = 75°, φ = 180 or 0° with a well depth of 271.078 cm-1 on the potential energy surface. The local minimum corresponding to a linear geometry is also found at R = 5.06 Å, θ1 = 2 or 178°, θ2 = 179°, φ = 0 or 180° with a well depth of 224.743 cm-1. The bound state calculations have been performed for the complex by approximating the N2 and OCS molecules as the rigid rotors. The calculated structural parameters and rotational transition frequencies are in good agreement with the experimental observed values. Based on the ab initio PES, the tunneling splitting is calculated to be 0.052 cm-1 for the ground vibrational state, which can just reproduce 64% of experimental observation (0.082 cm-1). A refined method is used to calculate the tunneling splitting, and a much better result is obtained with the value of 0.094 cm-1.

Solvation effects alter the photochemistry of 2-thiocytosine

Radiationless deactivation channels of 2-thiocytosine in aqueous environment are revisited by means of quantum-chemical simulations of excited-state absorption spectra, and investigations of potential energy surfaces of the chromophore clustered with two water molecules using the algebraic diagrammatic construction method to the second-order (ADC(2)), and multireference configuration interaction with single and double excitations (MR-CISD) methods. We argue that interactions of explicit water molecules with thiocarbonyl group might enable water-chromophore electron transfer (WCET) which leads to formation of intersystem crossing that was not considered previously. This is the first example of a WCET process occurring in the triplet manifold of electronic states. This phenomenon might explain nonradiative decay of the triplet state population observed in thiopyrimidines in the absence of molecular oxygen. According to our calculations this WCET process might also entail a subsequent, virtually barrierless, electron-driven proton transfer (EDPT) resulting in the formation of hydroxyl radical which could further participate in photohydration or deamination reactions.

Fission barriers from multidimensionally-constrained covariant density functional theories

In recent years, we have developed the multidimensionally-constrained covariant density functional theories (MDC-CDFTs) in which both axial and spatial reflection symmetries are broken and all shape degrees of freedom described by β λμ with even μ , such as β 20 , β 22 , β 30 , β 32 , β 40 , etc., are included self-consistently. The MDC-CDFTs have been applied to the investigation of potential energy surfaces and fission barriers of actinide nuclei, third minima in potential energy surfaces of light actinides, shapes and potential energy surfaces of superheavy nuclei, octupole correlations between multiple chiral doublet bands in 78 Br, octupole correlations in Ba isotopes, the Y 32 correlations in N = 150 isotones and Zr isotopes, the spontaneous fission of Fm isotopes, and shapes of hypernuclei. In this contribution we present the formalism of MDC-CDFTs and the application of these theories to the study of fission barriers and potential energy surfaces of actinide nuclei.

Derivation of Reliable Geometries in QM Calculations of DNA Structures: Explicit Solvent QM/MM and Restrained Implicit Solvent QM Optimizations of G-Quadruplexes

Modern dispersion-corrected DFT methods have made it possible to perform reliable QM studies on complete nucleic acid (NA) building blocks having hundreds of atoms. Such calculations, although still limited to investigations of potential energy surfaces, enhance the portfolio of computational methods applicable to NAs and offer considerably more accurate intrinsic descriptions of NAs than standard MM. However, in practice such calculations are hampered by the use of implicit solvent environments and truncation of the systems. Conventional QM optimizations are spoiled by spurious intramolecular interactions and severe structural deformations. Here we compare two approaches designed to suppress such artifacts: partially restrained continuum solvent QM and explicit solvent QM/MM optimizations. We report geometry relaxations of a set of diverse double-quartet guanine quadruplex (GQ) DNA stems. Both methods provide neat structures without major artifacts. However, each one also has distinct weaknesses. In restrained optimizations, all errors in the target geometries (i.e., low-resolution X-ray and NMR structures) are transferred to the optimized geometries. In QM/MM, the initial solvent configuration causes some heterogeneity in the geometries. Nevertheless, both approaches represent a decisive step forward compared to conventional optimizations. We refine earlier computations that revealed sizable differences in the relative energies of GQ stems computed with AMBER MM and QM. We also explore the dependence of the QM/MM results on the applied computational protocol.

Wave Function Frozen-Density Embedding: Coupled Excitations.

We report quasi-ab initio correlated ground-state and excitation-energy calculations for agglomerates consisting of several molecules with total system sizes of up to more than one hundred atoms using a combination of a density-fitted, approximate second-order coupled-cluster singles and doubles (RICC2) method and frozen-density embedding (FDE), denoted RICC2-in-RICC2. Working equations are presented for CC2 ground-state energies and approximate coupled excitation energies, which are a necessary prerequisite for investigations of potential energy surfaces (PESs) of both ground and excited states. The approach is applicable to all systems that can be decomposed into interacting individual molecules for which the RICC2 calculation itself is feasible. Because of the absence of exact exchange in the formalism and the possibility to efficiently evaluate Coulomb coupling integrals using density fitting or a dipole approximation, the coupling step is insignificant in terms of computation time.

Theoretical investigation of potential energy surface and bound states for the van der Waals complex Ar–BrCl dimer

The intermolecular potential energy surface (PES) of the ground electronic state for the Ar–BrCl dimer is constructed at the CCSD(T) level with the aug-cc-pVQZ basis set and mid-bond functions. The PES is characterized by three minima and two saddle points. The global minimum corresponding to a collinear Ar–BrCl configuration, which has been observed experimentally, is located at R=4.10Å and θ=2.5° with a well depth of −285.207cm−1. A nearly T-shaped structure and an anti-linear Ar–ClBr geometry is also predicted. The bound state calculations are preformed to study intermolecular vibrational modes, rotational levels and average structures for the complex. Our transition frequencies, spectroscopic constants and average structures for all isotopomers of the collinear isomer agree well with experimental data. We have also provided pure rotational transitional frequencies for both nearly T-shaped and anti-linear isomers. These results are significant for further experimental investigations of the Ar–BrCl dimer.

Global investigation of potential energy surfaces for the pyrolysis of C(1)-C(3) hydrocarbons: toward the development of detailed kinetic models from first principles.

Detailed kinetic models (DKMs) are the most fundamental "bottom-up" approaches to computational investigation of the pyrolysis and oxidation of fuels. The weakest points of existing DKMs are incomplete information about the reaction types that can be involved in the potential energy surfaces (PESs) in pyrolysis and oxidation processes. Also, the computational thermodynamic parameters available in the literature vary widely with the level of theory employed. More sophisticated models require improvement both in our knowledge of the type of the reactions involved and the consistency of thermodynamic and kinetic parameters. In this paper, we aim to address these issues by developing ab initio models that can be used to describe early stages of pyrolysis of C1-C3 hydrocarbons. We applied a recently developed global reaction route mapping (GRRM) strategy to systematically investigate the PES of the pyrolysis of C1-C3 hydrocarbons at a consistent level of theory. The reactions are classified into 14 reaction types. The critical points on the PES for all reactions in the network are calculated at the highly accurate UCCSD(T)-F12b/cc-pVTZ//UM06-2X/cc-pVTZ level of theory. The data reported in this paper can be used for first principle calculations of kinetic constants and for a subsequent study on modeling the evolution of the species from the reaction network of the pyrolysis and oxidation of C1-C3 hydrocarbons.

Reaction Mechanism and Catalytic Fingerprint of Allantoin Racemase.

The stereospecific oxidative decomposition of urate into allantoin is the core of purine catabolism in many organisms. The spontaneous decomposition of upstream intermediates and the nonenzymatic racemization of allantoin lead to an accumulation of (R)-allantoin, because the enzymes converting allantoin into allantoate are specific for the (S) isomer. The enzyme allantoin racemase catalyzes the reversible conversion between the two allantoin enantiomers, thus ensuring the overall efficiency of the catabolic pathway and preventing allantoin accumulation. On the basis of recent crystallographic and biochemical evidence, allantoin racemase has been assigned to the family of cofactor-independent racemases, together with other amino acid racemases. A detailed computational investigation of allantoin racemase has been carried out to complement the available experimental data and to provide atomistic insight into the enzymatic action. Allantoin, the natural substrate of the enzyme, has been investigated at the quantum mechanical level, in order to rationalize its conformational and tautomeric equilibria, playing a key role in protein-ligand recognition and in the following catalytic steps. The reaction mechanism of the enzyme has been elucidated through quantum mechanics/molecular mechanics (QM/MM) calculations. The potential energy surface investigation, carried out at the QM/MM level, revealed a stepwise reaction mechanism. A pair of cysteine residues promotes the stereoinversion of a carbon atom of the ligand without the assistance of cofactors. Electrostatic fingerprint calculations are used to discuss the role of the active site residues in lowering the pKa of the substrate. The planar unprotonated intermediate is compared with the enolic allantoin tautomer observed in the active site of the crystallized enzyme. Finally, the enzymatic catalysis featured by allantoin racemase (AllR) is compared with that of other enzymes belonging to the same family.

Computational identification of a global carbon–sulfur triply bonded isomer SCBO

Searching for stable sulfur–carbon triply bonded molecules has been of great interest from both the fundamental and applied viewpoints. The known polyatomic sulfur–carbon triply bonded molecules are usually not the global minima. Here, we report a potential energy surface investigation of a tetra-atomic molecule [S,C,B,O] in both doublet and quartet states. The B3LYP and M06-2X methodologies with 6-311+G(3df,2p) and aug-cc-pVTZ basis sets were applied for geometrical optimization and CCSD(T)/aug-cc-pVTZ for single-point energy calculations. The thermodynamically most stable isomer is the linear SCBO 01 (0.0 kcal/mol). Kinetically, SCBO 01 is separated from the other isomers and fragments by the rather high barriers of at least 44.7 kcal/mol. In particular, isomer SCBO 01 contains a typical carbon–sulfur triple bond based on the systematic analysis from the structure, vibrational frequency, molecular orbital, Wiberg bond index, and adiabatic bond dissociation energy. In addition, there exists a second low-lying isomer, i.e., linear SBCO 02 (7.3 kcal/mol) with S≡B triple bonding, whose kinetic stability is governed by its fragmentation to 2SB+1CO (30.4 kcal/mol). The remaining isomers are either kinetically unstable with low conversion barriers or energetically very high lying. We propose that the simple two-body association between SC and BO, SB and CO pairs can preferentially lead to the formation and stabilization of SCBO 01 and SBCO 02, respectively. The isomer SCBO 01, which is the global structure and extraordinarily stable against both isomerization and fragmentation, strongly deserves future laboratory studies.

Universal perturbative explicitly correlated basis set incompleteness correction

Basis set incompleteness error for an arbitrary approximate electronic wave function is robustly reduced using a second-order perturbative correction into a basis of explicitly correlated, internally contracted geminal functions. The Hylleraas functional for the second-order energy correction is evaluated algebraically involving at most a four-electron reduced density matrix and four-electron integrals. By using the R12 technology in combination with screening approximations such a correction only requires a two-electron reduced density matrix and two-electron integrals. Preliminary investigations of potential energy surfaces of hydrogen fluoride and nitrogen molecules at the multireference configuration interaction singles and doubles indicate that with the perturbative correction only an aug-cc-pVDZ basis is necessary to compute correlation energies of an aug-cc-pVQZ quality, or better. The proposed correction, dubbed [2](R12), can in principle be combined with any single reference and multireference method in use today.

Assessment of quantum chemical methods and basis sets for excitation energy transfer

The validity of several standard quantum chemical approaches and other models for the prediction of exciton energy transfer is investigated using the HOMO–LUMO excited states of benzene dimer as an example. The configuration interaction singles (CIS), time-dependent Hartree-Fock (TD-HF), time dependent density functional theroy (TD-DFT), and complete-active-space self-consistent-field (CASSCF) methods are applied with a supermolecule approach and compared to the previously established monomer transition density method and the ideal dipole approximation. Strong and physically incorrect admixture of charge-transfer states makes TD-DFT inappropriate for investigations of potential energy surfaces in such dimer systems. CIS, TD-HF and CASSCF perform qualitatively correct. TD-HF seems to be a particularly appropriate method due to its general applicability and overall good performance for the excited state and for transition properties. Double-zeta basis sets with polarisation functions are found to be sufficient to predict transfer rates of dipole allowed excitations. Efficient excitation energy transfer is predicted between degenerate excited states while avoided curve crossings of nearly spaced π-aggregates are identified as a possible trapping mechanism.

Singlet and triplet potential energy surfaces of C 3H 2

The detailed singlet and triplet potential energy surfaces of C 3H 2 involving nine isomers and 13 transition structures are studied at the G3 level of theory. The rearrangement mechanisms and the electronic properties of various isomers in a broad energy range have been studied in both singlet and triplet states. Cyclopropenylidene and propargylene are found to be the most stable isomers in the singlet and triplet states, respectively. The singlet isomers are found to be more kinetically stable species as a result of high conversion barriers through which they pass. The calculations indicate that cyclopropyne in its triplet state is the least kinetically stable isomer. It is realized that the G3 method comprises both computational cost and accuracy and thus can be applied to investigation of potential energy surface of small molecules.

A DFT investigation of potential energy surface and vibrational properties of hydrogen adsorbed on the Rh(1 1 1) surface

Vibrational properties of hydrogen on the Rh(1 1 1) surface have been investigated theoretically. The potential energy surface for this system has been calculated within the density functional theory. The potential is found to be very anharmonic. The wave functions and their energies for the hydrogen motion on the potential energy surface (PES) have been calculated and assigned by using discrete variable representation. It was found that the vibrational wave function is localized at hollow site in the ground state for hydrogen on Rh(1 1 1). Higher excited states are of delocalized nature and mixed parallel and perpendicular character. Our results are in good agreement with the observed vibrational spectra of hydrogen on the Rh(1 1 1) surface.

Following Reaction Pathways Using a Damped Classical Trajectory Algorithm

The study of reaction pathways is imperative to the investigation of potential energy surfaces. The intrinsic reaction coordinate is defined as the steepest descent path in mass weighted coordinates that connects the transition state to reactants and products. Various methods are available for following the intrinsic reaction coordinate. A potential energy surface may also be studied using classical trajectory calculations, and a dynamic reaction path method can be used to connect the transition state to reactants and products. We have modified a classical trajectory integration method such that the dynamic reaction pathway more closely resembles the intrinsic reaction coordinate. Specifically, a damped velocity Verlet algorithm incorporating a controlled time step is used. The efficiency of the present algorithm is on the same order as our earlier methods for relatively small systems and shows increasing efficiency as the large molecule limit is approached.

Ab initio study of O2 precursor states on the Pd(111) surface

Interactions of O and O2 with the Pd(111) surface are studied using spin-density-functional theory with gradient corrections. The investigation of potential energy surface of O atom on Pd(111) shows the face centered cubic site adsorption to be the most favorable. The diffusion barrier to an adjacent hexagonal closed pack site is 0.56 eV. Several adsorption trajectories are calculated for O2 on Pd(111). We find that the molecule dissociation is either direct but strongly activated or precursor mediated with considerably lower barrier. Three precursor states are found and identified according to geometry, energy, and vibrational frequency. Two precursor states are energetically degenerate with only slightly different geometries. Density difference analysis reveals that the electronic structure of both the molecule and the nearest Pd atoms is modified during the adsorption. However, according to density difference analysis the molecules in the precursor states are neutral and the interaction between O2 and the substrate resembles the donation–backdonation scheme.

Investigation of Potential Energy Surface of Thioformaldehyde-S-S-dioxide by MNDO Method

Potential energy surface of thioformaldehyde-S-S-dioxide (sulfene) was of complicated multiextremal character with minima corresponding to several isomers; the structure and interconversion thereof was studied by MNDO method. The structural dynamics of sulfene is the main reason of its abnormally high reactivity.

A theoretical investigation of potential energy surfaces governing the photochemical tautomerization of 2-pyridone

The kinetics and thermodynamics of lactam/lactim tautomerization in 2-pyridone through intramolecular proton transfer have been investigated for the lowest three singlet electronic states. All the energy extrema on the three surfaces have been located and the concerted reaction paths have been traced. Our results show that planar paths are followed in the ground and the first excited ππ* singlet, which are characterized by well-defined saddle points. Activation energies are large enough to preclude direct proton transfer, but the reverse process could be operative in the ππ * state. The concerted reaction path of the nπ * state shows an energy plateau in its central part, and it was not possible to locate a sharp saddle point. This opens up the possibility of a non-planar path in this state.