Two-dimensional Potential Energy Surface Research Articles

DFT/MM Simulations for Cycloreversion Reaction of Cyclobutane Pyrimidine Dimer with Deprotonated and Protonated E283.

DNA photolyase targets the primary ultraviolet (UV)-induced DNA lesion─cyclobutane pyrimidine dimer (CPD), attaches to it, and catalyzes its dissociation. The catalytic mechanism of DNA photolyase and the role of the conserved residue E283 remain subjects of debate. This study employs two-dimensional potential energy surface maps and minimum free energy paths calculated at the ωB97XD/6-31G/MM level to elucidate these mechanisms. Results suggest that the catalytic process follows a sequential, stepwise reaction in which the C5-C5 and C6-C6 bonds are cleaved in order, facilitated by a protonated E283. Activation free energies for these cleavages are calculated at 4.4 and 4.2 kcal·mol-1, respectively. Protonation of E283 reduces electrostatic repulsion with CPD and forms dual hydrogen bonds with it and provides better solvation, stabilizing the CPD radical anion, particularly during intermediate state. This stabilization renders the initial splitting step exergonic, slows reverse reactions of the C5-C5 bond cleavage and electron transfer, and ensures a high quantum yield. Furthermore, the protonation state of E283 significantly affects the type of bond cleavage. Other residues in the active site were also investigated for their roles in the mechanism.

DFT/MM Simulations for Cycloreversion Reaction of Cyclobutane Pyrimidine Dimer with Deprotonated and Protonated E283.

DNA photolyase targets the primary ultraviolet (UV)-induced DNA lesion─cyclobutane pyrimidine dimer (CPD), attaches to it, and catalyzes its dissociation. The catalytic mechanism of DNA photolyase and the role of the conserved residue E283 remain subjects of debate. This study employs two-dimensional potential energy surface maps and minimum free energy paths calculated at the ωB97XD/6-31G/MM level to elucidate these mechanisms. Results suggest that the catalytic process follows a sequential, stepwise reaction in which the C5-C5 and C6-C6 bonds are cleaved in order, facilitated by a protonated E283. Activation free energies for these cleavages are calculated at 4.4 and 4.2 kcal·mol-1, respectively. Protonation of E283 reduces electrostatic repulsion with CPD and forms dual hydrogen bonds with it and provides better solvation, stabilizing the CPD radical anion, particularly during intermediate state. This stabilization renders the initial splitting step exergonic, slows reverse reactions of the C5-C5 bond cleavage and electron transfer, and ensures a high quantum yield. Furthermore, the protonation state of E283 significantly affects the type of bond cleavage. Other residues in the active site were also investigated for their roles in the mechanism.

New rotational rate coefficients computation of MgC3N(X2Σ+) by collision with He(1S)

ABSTRACT Determining physical conditions in interstellar environments requires reliable estimation of collisional data for molecules detected in space. In this work, we report a rate coefficients calculation of MgC3N(X2Σ+) induced by collision with He. This study is based on a new 2D potential energy surface (2D-PES), obtained from the explicitly correlated restricted open-shell coupled cluster approach with single, double, and perturbative triple excitation (rccsd(t)-f12) and the aug-cc-pVTZ basis sets. The MgC3N–He PES presents a global minimum with a well depth of −45.6 cm−1. Based on this interaction potential, we derived the excitation cross-sections using the close-coupling quantum time-independent formalism for total energies ≤500 cm−1 and N ≤ 40. These cross-sections were then integrated on a Maxwell–Boltzmann distribution of kinetic energies to obtain the collisional (de)-excitation rate coefficients for thermal temperature below 100 K. A non-LTE radiative transfer calculation was performed using the present collisional rates in order to estimate their impact on the abundance of MgC3N. These collisional data can help astronomers for the detection and an accurate determination of MgC3N abundance in the investigated interstellar clouds.

A DFT study on photodissociation of the palladium tetrachloride anion PdCl42− in solution

Photodissociation of PdCl42− in water is investigated using the time-dependent DFT method with the polarized continuum model. First, to find out the exchange–correlation functional that can well describe the present system we make following two comparisons using many functionals: (i) the DFT absorption spectrum vs. experiment; (ii) the DFT one-dimensional (1D) potential energy curves (PECs) vs. the previous MRCI 1D PECs. As a result of comparison, it is found that the range-separated hybrid functionals well reproduce the observed spectrum and, among these, the M11 functional may be the most reasonable choice. Next, using M11, we calculate ground and excited-state 1D PECs for single Cl loss in water and the ground-state two-dimensional (2D) potential energy surface (PES) for double Cl loss in water. It is revealed in the 1D PECs in water that electronic excitations to the PECs that have large transition dipole moments with the ground electronic state may easily lead to the PdCl3− + Cl− dissociation channel, which is similar to single Cl loss in the gas phase. It is also found that the ground-state 2D PES in water correlates with the PdCl2 + 2Cl− dissociation channel with no transition state on the way to it. This is different from the prediction in the gas phase; the ground-state 2D PES correlates with the PdCl2 + Cl2− dissociation channel with a transition state on the minimum energy path leading to it.

Quantum study of the rovibrational relaxation of HF by collision with 4He on a new potential energy surface.

The HF molecule is considered the main reservoir of fluorine in the interstellar medium (ISM). Also, the interactions of this molecule with the most common atoms and molecules in the ISM have attracted great interest from the astrochemical community. Collisions between HF and helium have recently caused controversy following a study using a two-dimensional SAPT potential energy surface (PES) that exhibited large discrepancies with previous scattering calculations based on more recent ab initio potentials. To address this issue, our current work aims to develop the most precise three-dimensional PES for the HF+He system. We employ the size-consistent CCSD(T) method in conjunction with the aug-cc-pV6Z basis set. The main features of the new PES as well as the bound states of the He-HF complex are compared to the existing data. The new PES is then utilised to conduct close coupling calculations that demonstrate He-HF as a good instance of vibration-rotation near resonant energy transfer. The novel rate coefficients will be accessible via the BASECOL database, and the use of the new PES is advised when describing HF in helium droplets.

Cluster properties of heavy nuclei predicted with the Barcelona-Catania-Paris-Madrid energy density functional

We study the cluster emission properties of 224\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$^{224}$$\\end{document}Ra and 238\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$^{238}$$\\end{document}Pu employing the Barcelona-Catania-Paris-Madrid (BCPM) energy density functional (EDF). Starting from two-dimensional potential energy surfaces, coexisting fission paths are identified. A fission valley located at large octupole deformations, corresponding to a highly-asymmetric mass distribution, is found in both nuclei. As the corresponding fragments are dominated by the presence of 208\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$^{208}$$\\end{document}Pb, we can relate this fission path to the emergence of cluster emission. Using the octupole moment as collective degree of freedom, we compute the cluster decay half-lives and study the impact of collective inertias, pairing strength and collective zero-point energy. The agreement with experimental data resembles the results obtained for spontaneous fission half-lives, indicating the capability of BCPM to consistently describe a large variety of fission phenomena, including cluster emission.

Potential energy surface, Integral cross section and rate coefficients for collisions of [formula omitted] with He

We present a two-dimensional potential energy surface for the C4H−(X1Σ+)−He system, calculated with the internuclear C4H− distances frozen at the experimental minimum energy. Computations are carried out at the CCSD(T)-F12a level of theory with a aug-cc-pVTZ basis set. This potential surface presents a well depth of about −78.24cm−1 below the C4H−−He dissociation limit. The cross sections are obtained in the close coupling scheme and rate coefficients inferred by averaging the cross sections over a Maxwell–Boltzmann velocity distribution. A propensity towards Δj=1 transitions is observed.

Ab initio potential energy surface and anharmonic vibration spectrum of NF3+

Potential energy surfaces (PESs), vibrational frequencies, and infrared spectra are calculated for NF3+ using ab initio calculations, based on UCCSD(T)/cc-pVTZ combined with vibrational configuration interaction (VCI). Based on an iterative algorithm, the surfaces (SURF) program adds automatic points to the lattice representation of the potential function, the one-dimensional and two-dimensional PESs are calculated after reaching a convergence threshold, finally the smooth image of the potential energy surface is fitted. The PESs accurately account for the interaction between the different modes, with the mode q 6 symmetrical stretching vibrations having the greatest effect on the potential energy change of the whole system throughout the potential energy surface shift. The anharmonic frequencies are obtained when the VCI matrix is diagonalized. Fundamental frequencies, overtones, and combination bands of NF3+ are calculated, which generate the degenerate phenomenon between their frequencies. Finally, the calculated anharmonic frequency is used to plot the infrared spectra. Modal antisymmetric stretching ν 5 and symmetric stretching ν 6 exhibit a phenomenon of large-intensity borrowing. This study can provide data to support the characterization in the laboratory.

Theoretical re-investigation on the N–N bond breaking of N2O+ cations in the A2Σ+ and B2Π states at the CASPT2 level

Two-dimensional multistate potential energy surfaces along N–NO bond length and N–N–O bond angle of N2O+ in the A2Σ+ and B2Π states were calculated at the CASPT2/cc-pVQZ level. In comparison to the known decomposition mechanisms in linear structure, a new N–NO bond fission pathway was proposed in bent geometry for the A2Aʹ(A2Σ+) state with a lower barrier, leading to rotationally excited NO+(X1Σ+) and N(2D) fragments. Likewise, the respective contributions of the Aʹ and A″ components split from the B2Π state were clarified. Considering avoided crossing and the coupling of spin states, ro-vibrational distributions of the NO+ fragment ion observed in experiments are elucidated.

Rotational (de-)excitation of protonated tricarbon monosulfide HC3S+ by collision with helium atoms

A new two-dimensional potential energy surface of the interaction between HC3S+ molecule and helium atom is mapped using an explicitly correlated coupled cluster approach with a single, double and perturbative triple excitation-F12a approach with an augmented-correlation-consistent polarized valence triple-zeta Gaussian basis set. The deepest potential well is identified at θ = 95∘ and R = 6.0 bohr with a depth of 100.67 cm−1. Cross-sections are determined for total energy up to 300 cm−1 using a coupled states method. Thermal rate coefficients are derived from the determined cross-sections for temperatures ranging between 3 K and 50 K. A clear predominance of = 2 processes is observed.

Importance of surface morphology on secondary electron emission: a case study of Cu covered with carbon, carbon pairs, or graphitic-like layers

Understanding the relationship between surface adsorbates and secondary electronic emission is critical for a variety of technologies, since the secondary electrons can have deleterious effects on the operation of devices. The mitigation of such phenomena is desirable. Here, using the collective efforts of first-principles, molecular dynamics, and Monte Carlo simulations, we studied the effects of a variety of carbon adsorbates on the secondary electron emission of Cu (110). It was demonstrated that the adsorption of atomic C and C_2 pair layers can both reduce and increase the number of secondary electrons depending on the adsorbate coverage. It was shown that under electron irradiation, the C–Cu bonds can be dissociated and reformed into C_2 pairs and graphitic-like layers, in agreement with experimental observation. It was verified that the lowest secondary electron emission was due to the formation of the graphitic-like layer. To understand the physical reason for changes in number of secondary electrons for different systems from an electronic structure perspective, two-dimensional potential energy surfaces and charge density contour plots were calculated and analyzed. It was shown that the changes are strongly influenced by the Cu surface morphology and depends highly on the nature of the interactions between the surface Cu and C atoms.

Ground state and fission properties of even-A uranium isotopes from multidimensionally-constrained relativistic mean field model

The multidimensionally-constrained covariant density functional theories (MDC-CDFTs) have been developed to study the influence of octupole and triaxial deformations on the ground state and fission properties. In this paper, we present a brief review of the applications of MDC-CDFTs and discuss the results of a systematical study of even-[Formula: see text] uranium isotopes with the multidimensionally-constrained relativistic mean field (MDC-RMF) model which is one of the MDC-CDFTs with pairing correlations treated by using the Bardeen-Cooper-Schrieffer (BCS) approach. We examine in detail the two-dimensional potential energy surfaces [Formula: see text] of these U isotopes and discuss the ground state and fission properties as well as the third and fourth minima on the potential energy surfaces. The emphasis is put on the effects of octupole and triaxial deformations.

De-excitation rates of the newly discovered C5H+ in collision with He

ABSTRACT Collisional excitation of C5H+ by He was performed by mean of state-of-the-art methods. A high level of theory quantum chemical calculations were made to determine the interaction potential energy surface of C5H+ with helium. The new two-dimensional potential energy surface obtained from the RCCSD(T)-F12 ab initio approach associated with aug-cc-pVTZ basis sets, presents two minima below its dissociation limit with well depths of $-101.8$ and $-100.2\, \mathrm{cm}^{-1}$ . In order to derive accurate physical conditions from rotational transitions of the recently discovered C5H+ molecule in Taurus molecular cloud (TMC-1), rate coefficients calculations are performed. The C5H+(X1Σ+)–He de-excitation rates are obtained after averaging cross-sections for thermal temperature below 100 K. The integral cross-sections are computed with the close-coupling quantum time-independent formalism for $E\le 520 \, \mathrm{cm}^{-1}$ and J ≤ 15. The new collisional data will allow accurate determination of the C5H+ abundance and will help to understand the chemistry of carbon chain ions in the interstellar gas.

Diffusion in a two-dimensional energy landscape in the presence of dynamical correlations and validity of random walk model.

Diffusion in a multidimensional energy surface with minima and barriers is a problem of importance in statistical mechanics and it also has wide applications, such as protein folding. To understand it in such a system, we carry out theory and simulations of a tagged particle moving on a two-dimensional periodic potential energy surface, both in the presence and absence of noise. Langevin dynamics simulations at multiple temperatures are carried out to obtain the diffusion coefficient of a solute particle. Friction is varied from zero to large values. Diffusive motion emerges in the limit of a long time, even in the absence of noise. Noise destroys the correlations and increases diffusion at small friction. Diffusion thus exhibits a nonmonotonic friction dependence at the intermediate value of the damping, ultimately converging to our theoretically predicted value. The latter is obtained using the well-established relationship between diffusion and random walk. An excellent agreement is obtained between theory and simulations in the high-friction limit but not so in the intermediate regime. We explain the deviation in the low- to intermediate-friction regime using the modified random walk theory. The rate of escape from one cell to another is obtained from the multidimensional rate theory of Langer. We find that enhanced dimensionality plays an important role. To quantify the effects of noise on the potential-imposed coherence on the trajectories, we calculate the Lyapunov exponent. At small friction values, the Lyapunov exponent mimics the friction dependence of the rate.

Solving the Schrödinger equation of a planar model H4 molecule

The Schrödinger equation of a planar model H4 molecule was solved with the free complement (FC) - local Schrödinger equation (LSE) theory using the direct local sampling (DLS) method. Although this molecule is often used to examine the intrinsic weakness of the Hartree-Fock related theory, the present FC-LSE-DLS theory successfully produced accurate solutions of the Schrödinger equation at any geometries of this molecule. We mapped the two-dimensional potential energy surfaces and revealed that the ground state has a dissociation channel to a couple of H2 molecules but the two excited states have local minimums constructing H4 molecule.

An electric molecular motor

Macroscopic electric motors continue to have a large impact on almost every aspect of modern society. Consequently, the effort towards developing molecular motors1–3 that can be driven by electricity could not be more timely. Here we describe an electric molecular motor based on a [3]catenane4,5, in which two cyclobis(paraquat-p-phenylene)6 (CBPQT4+) rings are powered by electricity in solution to circumrotate unidirectionally around a 50-membered loop. The constitution of the loop ensures that both rings undergo highly (85%) unidirectional movement under the guidance of a flashing energy ratchet7,8, whereas the interactions between the two rings give rise to a two-dimensional potential energy surface (PES) similar to that shown by FOF1 ATP synthase9. The unidirectionality is powered by an oscillating10 voltage11,12 or external modulation of the redox potential13. Initially, we focused our attention on the homologous [2]catenane, only to find that the kinetic asymmetry was insufficient to support unidirectional movement of the sole ring. Accordingly, we incorporated a second CBPQT4+ ring to provide further symmetry breaking by interactions between the two mobile rings. This demonstration of electrically driven continual circumrotatory motion of two rings around a loop in a [3]catenane is free from the production of waste products and represents an important step towards surface-bound14 electric molecular motors.

Conformational Structures of Neutral and Cationic Pivaldehyde Revealed by IR-Resonant VUV-MATI Mass Spectroscopy

Pivaldehyde, which is an unwanted by-product released with engine exhaust, has received considerable research attention because of its hydrocarbon oxidations at atmospheric temperature. To gain insight into the conformer-specific reaction dynamics, we investigated the conformational structures of the pivaldehyde molecule in neutral (S0) and cationic (D0) states using the recently invented IR-resonant VUV-MATI mass spectroscopy. Additionally, we constructed the two-dimensional potential energy surfaces (2D PESs) associated with the conformational transformations in the S0 and D0 states to deduce the conformations corresponding to the measured vibrational spectra. The 2D PESs indicated the presence of only the eclipsed conformation in the global minima of both states, unlike those in propanal and isobutanal. However, comparing the IR-dip VUV-MATI spectra from two intense peaks in the VUV-MATI spectrum with the anharmonic IR simulations revealed the correspondence between the gauche conformer on the S0 state and the measured IR spectra. Furthermore, Franck-Condon analysis confirmed that most peaks in the VUV-MATI spectrum are attributed to the adiabatic ionic transitions between the neutral gauche and cationic eclipsed conformers in pivaldehyde. Consequently, electron removal from the highest occupied molecular orbital, consisting of the nonbonding orbital of the oxygen atom in pivaldehyde, promoted the formyl-relevant modes in the induced cationic eclipsed conformer.

An efficient error-correction model to investigate the rotational structure and microwave spectrum of Ar–AgF complex

• An error-correction model has been developed to predict the microwave spectra efficiently. • Due to the intramolecular effects included, the predicted transition frequencies were well reproduced with the error of 0.017%. • the intermolecular modes of Ar–AgF complex can be well described by an analogous form of Dunham series. An error-correction model has been developed to predict pure rotational spectrum of Ar–AgF complex. Firstly, based on the geometry optimizations, bond length was determined for AgF of free monomer and in Ar–AgF complex, respectively. Then, a scaled bond length for AgF was obtained by introducing the value of free monomer observed experimentally. Subsequently, a two-dimensional intermolecular potential energy surface (PES) was constructed for Ar–AgF complex. Due to the intramolecular effects included and bond length corrected in the PES, this model could well reproduce transition frequencies with an error of 0.017% for the microwave spectrum of Ar–AgF complex. Furthermore, a full-dimensional PES was also constructed for comparison, and results of bound state calculations produced an error of 0.029%, suggesting that the error-correction model is reliable and efficient according to the excellent agreement between theoretical and experimental results from transition frequencies and spectroscopic parameters.

Excited-state double proton transfer of 1,8-dihydroxy-2-naphthaldehyde: A MS-CASPT2//CASSCF study

Excited-state double proton transfer (ESDPT) is a controversial issue which has long been plagued with theoretical and experimental communities. Herein, we took 1,8-dihydroxy-2-naphthaldehyde (DHNA) as a prototype and used combined complete active space self-consistent field (CASSCF) and multi-state complete active-space second-order perturbation (MS-CASPT2) methods to investigate ES-DPT and excited-state deactivation pathways of DHNA. Three different tautomer minima of S1-ENOL, S1-KETO-1, and S1-KETO-2 and two crucial conical intersections of S1S0-KETO-1 and S1S0-KETO-2 in.and between the S0 and S1 states were obtained. S1-KETO-1 and S1-KETO-2 should take responsibility for experimentally observing dual-emission bands. In addition, two-dimensional potential energy surfaces (2D-PESs) and linear interpolated internal coordinate paths connecting relevant structures were calculated at the MS-CASPT2//CASSCF level and confirmed a stepwise ESDPT mechanism. Specifically, the first proton transfer from S1-ENOL to S1-KETO-1 is barrierless, whereas the second one from S1-KETO-1 to S1-KETO-2 demands a barrier of ca. 6.0 kcal/mol. The linear interpolated internal coordinate path connecting S1-KETO-1 (S1-KETO-2) and S1S0-KETO-1 (S1S0-KETO-2) is uphill with a barrier of ca. 12.0 kcal/mol, which will trap DHNA in the S1 state while therefore enabling dual-emission bands. On the other hand, the S1/S0 conical intersections would also prompt the S1 system to decay to the S0 state, which could be to certain extent suppressed by locking the rotation of the C5−C8−C9−O10 dihedral angle. These mechanistic insights are not only helpful for understanding ESDPT but also useful for designing novel molecular materials with excellent photoluminescent performances.

New de-excitation rates of the open shell dicarbon monoxide C2O(X3Σ−) in collision with He(1S)

Abstract In order to derive accurate physical conditions of the interstellar clouds (like TMC-1) from the rotational transitions of C2O, collisional rates are needed. Based on a new two-dimensional potential energy surface (2D-PES), we report a new rate coefficients calculation of C2O(X3Σ−) induced by collision with He. This PES was obtained from the explicitly correlated restricted open-shell coupled cluster with single, double and perturbative triple excitation (rccsd(t)-f12) ab initio approach associated with aug-cc-pVTZ basis sets. The C2O–He PES presents one minimum below its dissociation limit with a well depth of 42.376 cm−1. The close-coupling quantum time independent formalism was used to derive cross sections for E ≤ 370 cm−1 and N ≤ 10. De-excitation rate coefficients are obtained for thermal temperature below 80 K.