Diabatic Potential Energy Curves Research Articles

Proton-Coupled Electron Transfer upon Oxidation of Tyrosine in a De Novo Protein: Analysis of Proton Acceptor Candidates.

Redox-active residues, such as tyrosine and tryptophan, play important roles in a wide range of biological processes. The α3Y de novo protein, which is composed of three α helices and a tyrosine residue Y32, provides a platform for investigating the redox properties of tyrosine in a well-defined protein environment. Herein, the proton-coupled electron transfer (PCET) reaction that occurs upon oxidation of tyrosine in this model protein by a ruthenium photosensitizer is studied by using a vibronically nonadiabatic PCET theory that includes hydrogen tunneling and excited vibronic states. The input quantities to the analytical nonadiabatic rate constant expression, such as the diabatic proton potential energy curves and associated proton vibrational wave functions, reorganization energy, and proton donor-acceptor distribution functions, are obtained from density functional theory calculations on model systems and molecular dynamics simulations of the solvated α3Y protein. Two possible proton acceptors, namely, water or a glutamate residue in the protein scaffold, are explored. The PCET rate constant is greater when glutamate is the proton acceptor, mainly due to the more favorable driving force and shorter equilibrium proton donor-acceptor distance, although contributions from excited vibronic states mitigate these effects. Nevertheless, water could be the dominant proton acceptor if its equilibrium constant associated with hydrogen bond formation is significantly greater than that for glutamate. Although these calculations do not definitively identify the proton acceptor for this PCET reaction, they elucidate the conditions under which each proton acceptor can be favored. These insights have implications for tyrosine-based PCET in a wide variety of biochemical processes.

Collision integrals of electronically excited atoms in air plasmas. I. N–N and O–O interactions

The current work presents the collision integral data for N(4 S)–N(4 S, 2 D, 2 P) and O(3 P, 1 D, 1 S)–O(3 P, 1 D, 1 S) interactions in the temperature range of 500–50 000 K. The collision integrals are calculated based on high-quality potential energy curves (PECs) obtained from fitting the high-level calculation data in a wide energy range to the neural network (NN) functions. In the construction of PECs, the diabatic PECs are adopted when avoided crossings exist because the diabatic paths are much more likely to be followed for such situations. Moreover, the nonadiabatic transition effects are estimated to be negligible for PECs crossings. The accuracy of traditional analytical formulas to fit PECs are also examined. It is found that the collision integral calculations are sensitive to the accuracy of PECs and the NN based PECs overwhelm the others. The contribution of inelastic excitation exchange processes to the diffusion collision integrals are also computed by using an accurate evaluation of the differences of PECs for gerade and ungerade pairs of excited atoms. Finally, based on the new collision integral data, we calibrate the collision model parameters suitable for the widely used particle simulation methods. The collision integrals and collision models developed in this work can be used to support high-confidence simulations of weakly ionized air plasma problems.

Studies of mutual neutralization in collisions involving Mg+/H−, Na+/H−, Li+/H− and Li+/Cl−

The Landau-Zener model is used to systematically compute mutual neutralization cross sections for collisions between Mg+/H−, Na+/H−, Li+/H− and Li+/Cl−. Potential energy curves for electronic states that are relevant for mutual neutralization are taken from available literature. Where non-adiabatic couplings are available, they are utilized to compute the diabatic potential energy curves, crossing distance and electronic couplings. In cases where non-adiabatic couplings are not available, they are approximated using a Lorentzian function. The reaction cross sections are computed for the energy range 0.001 eV to 1000 eV. The results are compared with other available experimental and theoretical results and are found to be very comparable. There is an observable trend in the reaction cross section involving ions of metals and hydrogen at collision energies below 10 eV, with the heaviest metal showing the largest reaction cross section and the lightest metal with the lowest cross section. At collision energies below 10 eV, isotope effect is also found to have an effect on the reaction cross section for Li+/Cl−.

Compact and accurate ab initio valence bond wave functions for electron transfer: The classic but challenging covalent-ionic interaction in LiF

This paper combines the valence bond block diabatization approach with the idea of orbital breathing. With highly compact wave functions, the breathing orbital valence bond (BOVB) method is applied to investigate several atomic and molecular properties, including the electron affinity of F, the adiabatic and diabatic potential energy curves and the dipole moment curves of the two lowest-lying 1Σ+ states, the electronic coupling curve and the crossing distance of the two diabatic states, and the spectroscopic constants of the ground states for LiF. The configuration selection scheme proposed in this work is quite general, requiring only the selection of several de-excitation and excitation orbitals in a sense like the restricted active space self-consistent field method. Practically, this is also the first time that BOVB results are extrapolated to complete basis set limit. Armed with the chemical intuition provided by valence bond theory, the classic but challenging covalent-ionic interaction in the title molecule is not only conceptually interpreted but also accurately computed.

Theoretical Study of the FrLi Molecule: Computation of Adiabatic and Diabatic Potential Energy Curves, Spectroscopic Constants, Dipole Moment, Radiative Lifetime and Spectrum Absorption

Theoretical Study of the FrLi Molecule: Computation of Adiabatic and Diabatic Potential Energy Curves, Spectroscopic Constants, Dipole Moment, Radiative Lifetime and Spectrum Absorption

Diabatic potential energy curves for the ^4{Pi} states of SH

We present a diabatic representation of the potential energy curves (PECs) for the ^4{{Pi}} states of mathrm {SH}. Multireference, configuration interaction (MRCI) calculations were used to determine high-accuracy adiabatic PECs of both mathrm {SH} and {mathrm {SH}}^+ from which the diabatic representation is constructed for mathrm {SH}. The adiabatic PECs exhibit many avoided crossings due to strong Rydberg-valence mixing. We employ the block diagonalization method, an orthonormal rotation of the adiabatic Hamiltonian, to disentangle the valence autoionizing and Rydberg ^4Pi states of mathrm {SH} by constructing a diabatic Hamiltonian. The diagonal elements of the diabatic Hamiltonian matrix at each nuclear geometry render the diabatic PECs and the off-diagonal elements are related to the state-to-state coupling. Care is taken to assure smooth variation and consistency of chemically significant molecular orbitals across the entire geometry domain.

Theoretical study of the LiNa molecule beyond the Born–Oppenheimer approximation: adiabatic and diabatic potential energy curves, radial coupling, adiabatic correction, dipole moments and vibrational levels

ABSTRACTThe adiabatic potential energy curves for ground and many excited states of 1, 3Σ+, 1,3Π, 1,3Δ symmetries of the LiNa molecule have been performed. We have used an ab initio approach based on non-empirical pseudopotentials, parameterised l-dependent polarisation potentials and full configuration interaction calculations. In addition, the adiabatic potential energy curves determined in our previous work [Mabrouk and Berriche, J. Phys. B: At. Mol. Opt. Phys. 41, 155101 (2008).] are corrected by using a diabatisation procedure, based on the effective Hamiltonian theory and an effective metric. The diabatic permanent moments for first 10 1Σ+ electronic states show linear behaviours, especially at intermediate and large distance. The transition dipole moment between neighbour states has revealed many peaks located around the avoided crossing positions. The radial coupling between the adiabatic states was calculated using the Hellmann-Feynman formula and numerical differentiation of the rotation matrix. The first and the second derivatives revealed many peaks, associated to neutral-neutral and ionic-neutral crossings. Furthermore, the radial coupling is used to evaluate the adiabatic correction, which is found to be of an order of tens and hundreds of cm−1, especially of higher excited states. In addition, we have determined the vibrational level spacing for all studied states.

Adiabatic and Diabatic Investigation of Numerous Electronic States for the Alkali Dimer FrNa.

The current paper reports a global investigation of all excited states below the ionic limit Fr+Na- of FrNa molecule following diabatic and adiabatic representations. The adiabatic and diabatic potential energy curves (PECs) for Σ+, Π, and Δ symmetries have been calculated for a dense grid of internuclear distances. The transition and permanent dipole moments (TDM and PDM) have been reported for both representations. Regarding the pseudopotential approach and full valence configuration interaction (FCI), the ab initio computation has been performed. Furthermore, the diabatization method was achieved by the use of the variational effective Hamiltonian theory (VEH). This latter served to assess the nonadiabatic coupling between the treated adiabatic states and to eliminate it employing a suitable unitary transformation matrix. The detailed computation of the PECs and PDM and TDM curves of the ground and excited states play a key role to coordinate experimental efforts in order to create cold and ultracold molecules in their ground stable rovibrational levels.

Topological Effects in Vibronically Coupled Degenerate Electronic States: A Case Study on Nitrate and Benzene Radical Cation.

We carry out detailed investigation for topological effects of two molecular systems, NO3 radical and C6H6+ (Bz+) radical cation, where the dressed adiabatic, dressed diabatic, and adiabatic-via-dressed diabatic potential energy curves (PECs) are generated employing ab initio calculated adiabatic and diabatic potential energy surfaces (PESs). We have implemented beyond Born–Oppenheimer (BBO) theory for constructing smooth, single-valued, and continuous diabatic PESs for five coupled electronic states [J. Phys. Chem. A2017,121, 6314–6326]. In the case of NO3 radical, the nonadiabatic coupling terms (NACTs) among the low-lying five electronic states, namely, X̃2A2′ (12B2), A~2E″ (12A2 and 12B1), and B~2E′ (12A1 and 22B2), bear the signature of Jahn–Teller (JT) interactions, pseudo JT (PJT) interactions, and accidental conical intersections (CIs). Similarly, Bz+ radical cation also exhibits JT, PJT, and accidental CIs in the interested domain of nuclear configuration space. In order to generate dressed PECs, two components of degenerate in-plane asymmetric stretching modes are selectively chosen for both the molecular species (Q3x–Q3y pair for NO3 radical and Q16x–Q16y pair for Bz+ radical cation). The JT coupling between the electronic states is essentially originated through the asymmetric stretching normal mode pair, where the coupling elements exhibit symmetric and nonlinear functional behavior along Q3x and Q16x normal modes.

Diabatic investigation for the NaRb molecule

AbstractAn extensive diabatic investigation of the NaRb species has been carried out for all excited states up to the ionic limit Na‐Rb+. An ab initio calculation founded on the pseudopotential, core polarization potential operators and full configuration interaction has been used with an efficient diabatization method involving a combination of variational effective hamiltonian theory and an effective overlap matrix. Diabatic potential energy curves and electric dipole moments (permanent and transition) for all the symmetries Σ+, Π, and Δ have been studied for the first time. Thanks to a unitary rotation matrix, the examination of the diabatic permanent dipole moment (PDM) has shown the ionic feature clearly seen in the diabatic 1Σ+ potential curves and confirming the high imprint of the Na‐Rb+ ionic state in the adiabatic representation. Diabatic transition dipole moments have also been computed. Real crossings have been shown for the diabatic PDM, locating the avoided crossings between the corresponding adiabatic energy curves.

A theoretical study of the dissociative recombination of SH+ with electrons through the 2Π states of SH.

A quantitative theoretical study of the dissociative recombination of SH+ with electrons has been carried out. Multireference, configuration interaction calculations were used to determine accurate potential energy curves for SH+ and SH. The block diagonalization method was used to disentangle strongly interacting SH valence and Rydberg states and to construct a diabatic Hamiltonian whose diagonal matrix elements provide the diabatic potential energy curves. The off-diagonal elements are related to the electronic valence-Rydberg couplings. Cross sections and rate coefficients for the dissociative recombination reaction were calculated with a stepwise version of the multichannel quantum defect theory, using the molecular data provided by the block diagonalization method. The calculated rates are compared with the most recent measurements performed on the ion Test Storage Ring (TSR) in Heidelberg, Germany.

The DQ and DQΦ electronic structure diabatization methods: Validation for general applications.

We recently proposed the dipole-quadrupole (DQ) method for transforming adiabatic electronic states to diabatic states by using matrix elements of the dipole and quadrupole operators, and we applied the method to 3-state diabatizations of LiH and phenol. Here we extend the method to also include the electrostatic potential, and we call the resulting method the DQΦ method, which denotes the dipole-quadrupole-electrostatic-potential diabatization method. The electrostatic potential provides extra flexibility, and the goal of the present work is to test and illustrate the robustness of the methods for producing diabatic potential energy curves that tend to the adiabatic curves away from crossings and avoided crossings and are smooth in regions of crossings and avoided crossings. We illustrate the generality of the methods by an application to LiH with four states and by two-state diabatizations of HCl, (H2)2, O3, and the reaction Li + HF → LiF + H. We find that-if enough states are included-the DQ method does not have a significant dependence on the parameter weighting the quadrupole moment, and a geometry-independent value of 10 a0 (-2) is adequate in all cases tested. We also find that the addition of the electrostatic potential improves the diabatic potentials in some cases and provides an additional property useful for increasing the generality of the method for diabatization.

Multistate density function theory and the construction of diabatic and adiabatic potential energy surfaces

A multistate density function theory( MSDFT) based on valence bond theory was introduced. As an application,the MSDFT method was illustrated by the bond dissociation of H2 and the proton transfer between HNO3 and a water molecule. In the dissociation of H2,the MSDFT method yields a correct behavior as the two H atoms stretch to infinity,and gives a potential well in accord with second-order perturbation using complete active space( CASPT2). For the proton transfer process of HNO3,MSDFT can be used to yield both diabatic and adiabatic potential energy curves as a function of the proton transfer reaction coordinate. For the reaction barrier height,the inclusion of an ionic state in a three-state model can significantly improve the accuracy in barrier height in comparison with the high-level results.

Theoretical study of vibronic perturbations in magnesium carbide

ABSTRACTUnderstanding molecular systems with complex multi-configurational bonding has been of interest to both experimentalists and theoreticians for many years. High level dynamically weighted MRCI calculations were used to generate accurate potential energy curves for the triplet ground state 3Σ−, and triplet excited states up to (4 3Σ−, 4 3Π and 1 3Δ) and quintet (1 5Σ− and 1 5Π) states up to 50,000 cm−1 above the ground state minimum. The lowest four 3Π states of magnesium mono-carbide (MgC) are strongly coupled leading to lifetimes that are shortened by pre-dissociation for most of the vibronic states. Non-adiabatic derivative couplings between the 3Π states were used to determine diabatic potential energy curves. The state mixing role of spin–orbit coupling, which is much weaker than the non-adiabatic interactions, is discussed. A coupled vibronic Hamiltonian was solved to compute and assign strongly mixed vibronic states. The results are compared and contrasted with the valence iso-electronic beryllium carbide (BeC) system whose results were published earlier [B.J. Barker, I.O. Antonov, J.M. Merritt, V.E. Bondybey, M.C. Heaven, and R. Dawes, J. Chem. Phys. 137, 214313 (2012)]. Transitions, spectroscopic constants and band origins are expected to aid experimental detection of MgC in the future.

Reaction of associative ionization [formula omitted] at slow collisions of atoms

The endothermic reaction of associative ionization of nitrogen and oxygen atoms was studied in the case of slow atom collisions in the framework of multichannel quantum defect theory. The diabatic potential energy curves of the NО molecule excited states were calculated using multireference configuration interaction methods implemented in MOLPRO package. It was shown that cross section dependence on the energy of the colliding atoms is in a good agreement with the experiment. The rate coefficient of the reaction was defined at the temperature 100K⩽T⩽1000K range. The obtained data may be used for calculating the tiered kinetics of highly excited Rydberg state population in low-temperature plasma.

Theoretical study of the CsNa molecule: adiabatic and diabatic potential energy and dipole moment.

The adiabatic and diabatic potential energy curves of the low-lying electronic states of the NaCs molecule dissociating into Na (3s, 3p) + Cs (6s, 6p, 5d, 7s, 7p, 6d, 8s, 4f) have been investigated. The molecular calculations are performed using an ab initio approach based on nonempirical pseudopotential, parametrized l-dependent polarization potentials and full configuration interaction calculations through the CIPCI quantum chemistry package. The derived spectroscopic constants (Re, De, Te, ωe, ωexe, and Be) of the ground state and lower excited states are compared with the available theoretical and experimental works. Moreover, accurate permanent and transition dipole moment have been determined as a function of the internuclear distance. The adiabatic permanent dipole moment for the first nine (1)Σ(+) electronic states have shown both ionic characters associated with electron transfer related to Cs(+)Na(-) and Cs(-)Na(+) arrangements. By a simple rotation, the diabatic permanent dipole moment is determined and has revealed a linear behavior, particularly at intermediate and large distances. Many peaks around the avoided crossing locations have been observed for the transition dipole moment between neighbor electronic states.

Dynamic simulations of stimuli-responsive switching of azobenzene derivatives in self-assembled monolayers: reactive rotation potential and switching functions

Although the force field (FF)-based molecular dynamics (MD) simulation has been widely applied to rationalise the experimental observations and measurements in chemistry, physics, materials and life science for years, traditional FF suffers from the incapability for describing chemical reactions, which are crucial in many important transformation processes. In order to simulate the collective switching process in azobenzene-based self-assemble monolayers on Au(111) surface, reactive MD simulations with alternative FF were implemented. The classic torsion function has been modified to depict the diabatic potential energy curves for cis and trans isomers, respectively. A switching function is further introduced to connect two N = N rotation functions, and the surface hopping between the cis and trans curves is allowed. By using the reactive rotation potential and switching function, the collective effect of numerous reaction centres and the influence of environment on the quantum yield in the complex system were explored at mesoscopic dimension and timescales. The reactive FF may be also applicable for other complicated systems containing stilbene derivatives. Limitation and perspective for further developments for the other complicated reactions are also addressed.

Dissociation and dissociative ionization of H2+using the time-dependent surface flux method

The time-dependent surface flux method developed for the description of electronic spectra [L. Tao and A. Scrinzi, New J. Phys. 14, 013021 (2012); A. Scrinzi, New J. Phys. 14, 085008 (2012)] is extended to treat dissociation and dissociative ionization processes of H${}_{2}{}^{+}$ interacting with strong laser pulses. By dividing the simulation volume into proper spatial regions associated with the individual reaction channels and monitoring the probability flux, the joint energy spectrum for the dissociative ionization process and the energy spectrum for dissociation is obtained. The methodology is illustrated by solving the time-dependent Schr\"odinger equation for a collinear one-dimensional model of H${}_{2}{}^{+}$ with electronic and nuclear motions treated exactly and validated by comparison with published results for dissociative ionization. The results for dissociation are qualitatively explained by analysis based on dressed diabatic Floquet potential energy curves, and the method is used to investigate the breakdown of the two-surface model.

Structural and Spectroscopic Study of the LiRb Molecule beyond the Born–Oppenheimer Approximation

Adiabatic and diabatic potential energy curves and the permanent and transition dipole moments of the low-lying electronic states of the LiRb molecule dissociating into Rb(5s, 5p, 4d, 6s, 6p, 5d, 7s, 6d) + Li(2s, 2p) have been investigated. The molecular calculations are performed with an ab initio approach based on nonempirical pseudopotentials for Rb(+) and Li(+) cores, parametrized l-dependent core polarization potentials and full configuration interaction calculations. The derived spectroscopic constants (R(e), D(e), T(e), ω(e), ω(e)x(e), and B(e)) of the ground state and lower excited states are in good agreement with the available theoretical works. However, the 8-10(1)Σ(+), 8-10(3)Σ(+), 6(1,3)Π, and 3(1,3)Δ excited states are studied for the first time. In addition, to the potential energy, accurate permanent and transition dipole moments have been determined for a wide interval of internuclear distances. The permanent dipole moment of LiRb has revealed ionic characters both relating to electron transfer and yielding Li(-)Rb(+) and Li(+)Rb(-) arrangements. The diabatic potential energy for the (1,3)Σ(+), (1,3)Π, and (1,3)Δ symmetries has been performed for this molecule for the first time. The diabatization method is based on variational effective Hamiltonian theory and effective metric, where the adiabatic and diabatic states are connected by an appropriate unitary transformation.

Ab Initio Adiabatic and Diabatic Energies and Dipole Moments of the CaH+ Molecular Ion

The diabatic and adiabatic potential-energy curves and permanent and transition dipole moments of the highly excited states of the CaH(+) molecular ion have been computed as a function of the internuclear distance R for a large and dense grid varying from 2.5 to 240 au. The adiabatic results are determined by an ab initio approach involving a nonempirical pseudopotential for the Ca core, operatorial core-valence correlation, and full valence configuration interaction. The molecule is thus treated as a two-electron system. The diabatic potential energy curves have been calculated using an effective metric combined to the effective Hamiltonian theory. The diabatic potential-energy curves and their permanent dipole moments for the (1)∑(+) symmetry are examined and corroborate the high imprint of the ionic state in the adiabatic representation. Taking the benefit of the diabatization approach, correction of hydrogen electron affinity was taken into account leading to improved results for the adiabatic potentials but also the permanent and transition electric dipole moments.