Trajectory-based nonadiabatic molecular dynamics without calculating nonadiabatic coupling in the avoided crossing case: trans↔cis photoisomerization in azobenzene.

We develop a novel method to simulate analytical nonadiabatic switching probability based on effective coupling and effective collision energy by using only electronic adiabatic potential energy surfaces and its gradients in the case of avoided crossing types of nonadiabatic transitions. In addition, the present method can keep the same time step for computing both on-the-fly trajectory and nonadiabatic transitions accurately. The present method is most useful for localized nonadiabatic transitions induced by conical intersection. We employ the on-the-fly surface hopping algorithm with an ab initio quantum chemistry calculation to demonstrate a dynamic simulation for photoisomerization in azobenzene. Simulated quantum yield and lifetime converge to 0.39 and 53 femtosecond, respectively (0.33 and 0.81 picosecond) for cis-to-trans (trans-to-cis) photoisomerization with up to 800 (600) sampling trajectories. The present results agree well with those of the experiment, as well as results simulated with use of nonadiabatic coupling within Tully's fewest switching method. The present trajectory-based nonadiabatic molecular dynamics free from nonadiabatic coupling greatly enhances the simulation power of molecular dynamics for large complex chemical systems.

Landscapes of four-enantiomer conical intersections for photoisomerization of stilbene: CASSCF calculation.

The photoisomerization of cis- and trans-stilbene through conical intersections (CI) is mainly governed by four dihedral angles around central C═C double bonds. The two of them are C-C═C-C and H-C═C-H dihedral angles that are found to form a mirror rotation coordinate, and the mirror plane appears at the two dihedral angles equal to zeros with which the middle state is defined through partial optimization. There exist the first-type of hula-twist-CI enantiomers, the second-type of hula-twist-CI enantiomers, the first-type of one-bond-flip-CI enantiomers, and the second type of one-bond-flip-CI enantiomers as well as cis-enantiomers and trans-enantiomers with respect to this mirror plane. The complete active space self-consistent field method is employed to calculate minimum potential energy profile along the mirror rotation coordinate for each enantiomers, and it is found that the left-hand manifold and the right-hand manifold of potential energy surfaces can be energetically transferred via photoisomerization. Furthermore, two-dimensional potential energy surfaces in terms of the branching plane g-h coordinates are constructed at vicinity of each conical intersection, and the landscapes of conical intersections show distinct feature, and in excited-state four potential wells separated in different section of g-h plane related to different conical intersections which indicate different photoisomerization pathways.

New schemes for internally contracted multi-reference configuration interaction.

In this work we present a new internally contracted multi-reference configuration interaction (MRCI) scheme by applying the graphical unitary group approach and the hole-particle symmetry. The latter allows a Distinct Row Table (DRT) to split into a number of sub-DRTs in the active space. In the new scheme a contraction is defined as a linear combination of arcs within a sub-DRT, and connected to the head and tail of the DRT through up-steps and down-steps to generate internally contracted configuration functions. The new scheme deals with the closed-shell (hole) orbitals and external orbitals in the same manner and thus greatly simplifies calculations of coupling coefficients and CI matrix elements. As a result, the number of internal orbitals is no longer a bottleneck of MRCI calculations. The validity and efficiency of the new ic-MRCI code are tested by comparing with the corresponding WK code of the MOLPRO package. The energies obtained from the two codes are essentially identical, and the computational efficiencies of the two codes have their own advantages.

Are polynuclear superhalogens without halogen atoms probable? A high-level ab initio case study on triple-bridged binuclear anions with cyanide ligands.

The first theoretical exploration of superhalogen properties of polynuclear structures based on pseudohalogen ligand is reported here via a case study on eight triply-bridged [Mg2(CN)5](-) clusters. From our high-level ab initio results, all these clusters are superhalogens due to their high vertical electron detachment energies (VDE), of which the largest value is 8.67 eV at coupled-cluster single double triple (CCSD(T)) level. Although outer valence Green's function results are consistent with CCSD(T) in most cases, it overestimates the VDEs of three anions dramatically by more than 1 eV. Therefore, the combined usage of several theoretical methods is important for the accuracy of purely theoretical prediction of superhalogen properties of new structures. Spatial distribution of the extra electron of high-VDE anions here indicates two features: remarkable aggregation on bridging CN units and non-negligible distribution on every CN unit. These two features lower the potential and kinetic energies of the extra electron respectively and thus lead to high VDE. Besides superhalogen properties, the structures, relative stabilities and thermodynamic stabilities with respect to detachment of CN(-1) were also investigated for these anions. The collection of these results indicates that polynuclear structures based on pseudohalogen ligand are promising candidates for new superhalogens with enhanced properties.

Topology of conical/surface intersections among five low-lying electronic states of CO2: multireference configuration interaction calculations.

Multi-reference configuration interaction with single and double excitation method has been utilized to calculate the potential energy surfaces of the five low-lying electronic states (1)A1, (1)A2, (3)A2, (1)B2, and (3)B2 of carbon dioxide molecule. Topology of intersections among these five states has been fully analyzed and is associated with double-well potential energy structure for every electronic state. The analytical potential energy surfaces based on the reproducing kernel Hilbert space method have been utilized for illustrating topology of surface crossings. Double surface seam lines between (1)A1 and (3)B2 states have been found inside which the (3)B2 state is always lower in potential energy than the (1)A1 state, and thus it leads to an angle bias collision dynamics. Several conical∕surface intersections among these five low-lying states have been found to enrich dissociation pathways, and predissociation can even prefer bent-geometry channels. Especially, the dissociation of O((3)P) + CO can take place through the intersection between (3)B2 and (1)B2 states, and the intersection between (3)A2 and (1)B2 states.

Are trinuclear superhalogens promising candidates for building blocks of novel magnetic materials? A theoretical prospect from combined broken-symmetry density functional theory and ab initio study.

The structures, relative stabilities, vertical electron detachment energies, and magnetic properties of a series of trinuclear clusters are explored via combined broken-symmetry density functional theory and ab initio study. Several exchange-correlation functionals are utilized to investigate the effects of different halogen elements and central atoms on the properties of the clusters. These clusters are shown to possess stronger superhalogen properties than previously reported dinuclear superhalogens. The calculated exchange coupling constants indicate the antiferromagnetic coupling between the transition metal ions. Spin density analysis demonstrates the importance of spin delocalization in determining the strengths of various couplings. Spin frustration is shown to occur in some of the trinuclear superhalogens. The coexistence of strong superhalogen properties and spin frustration implies the possibility of trinuclear superhalogens working as the building block of new materials of novel magnetic properties.

Light response of gametophyte in Adiantum flabellulatum: transcriptome analysis and identification of key genes and pathways.

Light serves not only as a signaling cue perceived by plant photoreceptors but also as an essential energy source captured by chloroplasts. However, excessive light can impose stress on plants. Fern gametophytes possess the unique ability to survive independently and play a critical role in the alternation of generations. Due to their predominantly shaded distribution under canopies, light availability becomes a limiting factor for gametophyte survival, making it imperative to investigate their response to light. Previous research on fern gametophytes' light response has been limited to the physiological level. In this study, we examined the light response of Adiantum flabellulatum gametophytes under different photosynthetic photon flux density (PPFD) levels and identified their high sensitivity to low light. We thereby determined optimal and stress-inducing light conditions. By employing transcriptome sequencing, weighted gene co-expression network analysis, and Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses, we identified 10,995 differentially expressed genes (DEGs). Notably, 3 PHYBs and 5 Type 1 CRYs (CRY1s) were significantly down-regulated at low PPFD (0.1 µmol m-2 s-1). Furthermore, we annotated 927 DEGs to pathways related to photosynthesis and 210 to the flavonoid biosynthesis pathway involved in photoprotection. Additionally, we predicted 34 transcription factor families and identified a close correlation between mTERFs and photosynthesis, as well as a strong co-expression relationship between MYBs and bHLHs and genes encoding flavonoid synthesis enzymes. This comprehensive analysis enhances our understanding of the light response of fern gametophytes and provides novel insights into the mechanisms governing their responses to light.

The magnetic coupling in manganese-based dinuclear superhalogens and their analogues. A theoretical characterization from a combined DFT and BS study.

The structures, relative stabilities, vertical detachment energies and magnetic coupling properties of a series of manganese-based dinuclear superhalogens and their isoelectronic analogues are explored via a combined density functional theory and broken symmetry study. Both the capabilities of various exchange-correlation functionals and basis set effects are investigated. The large magnitudes of the calculated exchange coupling constants indicate clearly the apparent molecular magnetism of these new types of superhalogen. Encouragingly, the high possibility of the coexistence of both high stability and strong magnetic coupling in these new polynuclear superhalogens is also confirmed. Besides these, the larger magnitudes of the calculated coupling constants of iron-based clusters here, compared with the homodinuclear [Mn(2)Cl(5)](-) cluster, demonstrate the possibility of the existence of strong magnetic coupling in potential iron-based homo- and heterodinuclear superhalogens. The analysis of spin density distribution is also performed in order to understand the coupling mechanisms.

New implementation of the configuration-based multi-reference second order perturbation theory.

We present an improved version of the configuration-based multi-reference second-order perturbation approach (CB-MRPT2) according to the formulation of Lindgren on perturbation theory of a degenerate model space. This version involves a reclassification of the perturbation functions and new algorithms to calculate matrix elements in the perturber energy expressions utilizing the graphical unitary group approach and the hole-particle symmetry. The diagonalize-then-perturb (DP), including Rayleigh-Schrödinger and Brillouin-Wigner, and diagonalize-then-perturb-then-diagonalize (DPD) modes have been implemented. The new CB-MRPT2 method is applied to several typical and interesting systems: (1) the vertical excitation energies for several states of CO and N(2), (2) energy comparison and timing of the ground state of C(4)H(6), (3) the quasi-degeneracy of states in LiF, (4) the intruder state problems of AgH, and (5) the relative energies of di-copper-oxygen-ammonia complex isomers. The results indicate that the computational accuracy and efficiency of the presented methods are competitive and intruder-free. It should be emphasized that the DPD method rectifies naturally the shortcomings of LiF potential energy curves constructed by the original second order complete active space perturbation theory (CASPT2), without having to recourse to the so-called state mixture. Unlike CASPT2, the new methods give the same energy ordering for the two di-copper-oxygen-ammonia isomers as the previous multi-reference configuration interaction with single and double excitations methods. The new CB-MRPT2 method is shown to be a useful tool to study small to medium-sized systems.

NCAPG Promotes Tumor Progression and Modulates Immune Cell Infiltration in Glioma.

Glioma is one of the most deadly types of brain cancer. As it is highly invasive, the prognosis for glioma patients remains dismal, with median survival rarely exceeding 16 months. Thus, developing a new prognostic biomarker for glioma and investigating its molecular mechanisms is necessary for the development of an efficient treatment strategy. In this study, we analyzed a cohort of 1,131 glioma patients using RNA-seq data from The Cancer Genome Atlas (TCGA project) and Gene Expression Omnibus (GSE4290 and GSE16011 datasets), and validated the results using the RNA-seq data of 1,018 gliomas from the Chinese Glioma Genome Atlas (CGGA project). We used the R language as the main tool for statistical analysis and data visualization. We found that NCAPG, a mitosis-associated chromosomal condensing protein, is highly expressed in glioma tissues. Furthermore, the expression of NCAPG increased significantly with the increase in tumor grade, and high NCAPG expression was found to be a predictor of poor overall survival in glioma patients (P < 0.001). This result shows that NCAPG expression could be an independent prognostic factor. Importantly, when the expression of NCAPG was knocked down, the CCK-8 assay revealed that the proliferation of glioma cells (LN-229 and T98G cell lines) decreased significantly compared with the control group. In addition, the healing rates of these cells were significantly lower in the si-NCAPG group than in the control group (P < 0.001). We then used the CIBERSORT algorithm to analyze the expression levels of 22 subpopulations of immune cells and found that NCAPG was significantly negatively correlated with natural killer cell activation. In addition, it was positively correlated with MHC-I molecules and ADAM17. Our study is first in comprehensively describing the high expression of NCAPG in glioma. It also shows that NCAPG can function as an independent prognostic predictor of glioma, and that targeting NCAPG can be a new strategy for the treatment of glioma patients.

Theoretical studies on the mechanism and stereoselectivity of Rh(Phebox)-catalyzed asymmetric reductive aldol reaction.

Density functional theory calculations (B3LYP) have been carried out to understand the mechanism and stereochemistry of an asymmetric reductive aldol reaction of benzaldehyde and tert-butyl acrylate with hydrosilanes catalyzed by Rh(Phebox-ip)(OAc)(2)(OH(2)). According to the calculations, the reaction proceeds via five steps: (1) oxidative addition of hydrosilane, (2) hydride migration to carbon-carbon double bond of tert-butyl acrylate, which determines the chirality at C2, (3) tautomerization from rhodium bound C-enolate to rhodium bound O-enolate, (4) intramolecular aldol reaction, which determines the chirality at C3 and consequently the anti/syn-selectivity, and (5) reductive elimination to release aldol product. The hydride migration is the rate-determining step with a calculated activation energy of 23.3 kcal mol(-1). In good agreement with experimental results, the formation of anti-aldolates is found to be the most favorable pathway. The observed Si-facial selectivity in both hydride migration and aldol reaction are well-rationalized by analyzing crucial transition structures. The Re-facial attack transition state is disfavored because of steric hindrance between the isopropyl group of the catalyst and the tert-butyl acrylate.

Electronic structure calculations of low-lying electronic states of O3.

Configuration-based multi-reference second order perturbation theory (CB-MRPT2) and multi-reference configuration interaction with single and double excitations (MRCISD) have been used to calculate the bending and dissociation potential energy curves (PECs) of ozone. Based on these PECs, equilibrium structures, vertical and adiabatic transition energies of the ground state and several low-lying excited states, as well as intersections and avoided crossings among the states displayed on the PECs are investigated. The energy separation of the open and ring structures and the dissociation energy of the ground state X(1)A(1) are determined by reference-selected MRCISD. Furthermore, one-dimensional cuts along the dissociation reaction coordinate for the lowest four electronic states of O(3) with (1)A' symmetry and possible pre-dissociations are studied. The Hartley band may be pre-dissociable, and the pre-dissociation limit is found to be 3871 cm(-1), which corresponds to symmetric stretching quanta n(ss) ≈ 6.

New implementations of MRCI in semiempirical frameworks.

Multireference configuration interaction with single and double excitations (MRCISD) as well as its analytic CI gradients has been implemented in the semiempirical framework. The hole-particle symmetry and a mixed driven model for computing coupling coefficients have been used in the new code that allows us to perform MRCI and gradient calculations with higher efficiency and less storage requirements.

Potential energy curves and interpretation of electronic spectrum of the rhodium monoxide.

Potential energy curves of 17 electronic states of rhodium monoxide (RhO) are calculated by multireference configuration interaction with single and double excitations (MRCISD). The ground state of RhO is determined to be a (4)Sigma(-) state with equilibrium bond length of 1.710 A and harmonic vibrational frequency of 825 cm(-1) at the MRCISD level of theory. It dissociates into Rh((4)F)+O((3)P) with a dissociation energy of 3.77/4.26 eV (MRCISD/MRCISD+Q), which is in agreement with the experimental value of 4.19+/-0.43 eV. Two low-lying excited states a (2)Sigma(-) and b(2)Pi are located at 4152 and 7154 cm(-1) above the ground state. The b(2)Pi with the adjacent (2)Delta, (4)Delta, and (2)Pi(II) states can be strongly coupled via spin-orbit interaction leading to a large splitting between b (2)Pi(3/2)-b (2)Pi(1/2) states with the value of 2422 cm(-1), which is comparable with the experimental value of 2400 cm(-1). Two higher doublets, c(2)Pi and d(2)Pi, have the same dominant configuration, 10sigma(2)11sigma(2)12sigma(1)5pi(4)6pi(3)2delta(3), and their transitions to the ground state, i.e., c(2)Pi-->(4)Sigma(-) and d(2)Pi-->(4)Sigma(-), correspond to the two visible bands of RhO.

Detailed dynamics of the nonradiative deactivation of adenine: a semiclassical dynamics study.

A realistic dynamics simulation study is reported for the ultrafast radiationless deactivation of 9H-adenine. The simulation follows two different excitations induced by two 80 fs (fwhm) laser pulses that are different in energy: one has a photon energy of 5.0 eV, and the other has a photon energy of 4.8 eV. The simulation shows that the excited molecule decays to the electronic ground state from the (1)pipi* state in both excitations but through two different radiationless pathways: in the 5.0 eV excitation, the decay channel involves the out-of-plane vibration of the amino group, whereas in the 4.8 eV excitation, the decay strongly associates with the deformation of the pyrimidine at the C 2 atom. The lifetime of the (1) npi* state determined in the simulation study is 630 fs for the 5.0 eV excitation and 1120 fs for the 4.8 eV excitation. These are consistent with the experimental values of 750 and 1000 fs. We conclude that the experimentally observed difference in the lifetime of the (1) npi* state at various excitations results from the different radiationless deactivation pathways of the excited molecule to the electronic ground state.

Nonadiabatic simulation study of photoisomerization of azobenzene: detailed mechanism and load-resisting capacity.

Nonadiabatic dynamical simulations were carried out to study cis-to-trans isomerization of azobenzene under laser irradiation and/or external mechanical loads. We used a semiclassical electron-radiation-ion dynamics method that is able to describe the coevolution of the structural dynamics and the underlying electronic dynamics in a real-time manner. It is found that azobenzene photoisomerization occurs predominantly by an out-of-plane rotation mechanism even under a nontrivial resisting force of several tens of piconewtons. We have repeated the simulations systematically for a broad range of parameters for laser pulses, but could not find any photoisomerization event by a previously suggested in-plane inversion mechanism. The simulations found that the photoisomerization process can be held back by an external resisting force of 90-200 pN depending on the frequency and intensity of the lasers. This study also found that a pure mechanical isomerization is possible from the cis-to-trans state if the azobenzene molecule is stretched by an external force of approximately 1250-1650 pN. Remarkably, the mechanical isomerization first proceeds through a mechanically activated inversion, and then is diverted to an ultrafast downhill rotation that accomplishes the isomerization. Implications of these findings to azobenzene-based nanomechanical devices are discussed.

Pyrolysis mechanism of carbon matrix precursor cyclohexane--the formation of condensed-ring aromatics and the growing process of molecules.

Based on the experiments, the UAM1 method was adopted to investigate benzene condensation of an important intermediate and the molecule growing mechanism during the cyclohexane pyrolysis process. The conclusions were drawn as follows: (1) from the viewpoint of thermodynamics, the condensation of benzene and C4H5* is a spontaneous reaction and the rising temperature will increase the spontaneous tendency of the reaction. (2) From the viewpoint of kinetic, the condensation of benzene and C4H5* is a two-step reaction. The rate-determining step is step 2 of hydrogen removal from intermediate C10H10 (I1) with the activation energy of 350.61 kJ/mol below 1473 K while the rate-determining step is step 1 that free radical C4H5* attacks benzene to form intermediate C10H10 (I1) with the activation energy DeltaE(0)(not equal to theta)=31.74 kJ/mol above 1473 K. (3) The space structure, electronic structure and thermodynamics parameters of molecular reaction of dense-ring aromatizing compounds can be used to replace the resonance energy and free valence to judge the activation of thermodynamic reaction of compounds. And (4) the analysis of the space structure, electronic structure and thermodynamic parameters show that the growing process of molecules with benzene used as initial reactants becomes more easier as the multi-ring aromatizing molecular system increases.

Combined DFT and BS study on the exchange coupling of dinuclear sandwich-type POM: comparison of different functionals and reliability of structure modeling.

The exchange coupling of a group of three dinuclear sandwich-type polyoxomolybdates [MM'(AsMo7O27)2](12-) with MM' = CrCr, FeFe, FeCr are theoretically predicted from combined DFT and broken-symmetry (BS) approach. Eight different XC functionals are utilized to calculate the exchange-coupling constant J from both the full crystalline structures and model structures of smaller size. The comparison between theoretical values and accurate experimental results supports the applicability of DFT-BS method in this new type of sandwich-type dinuclear polyoxomolybdates. However, a careful choice of functionals is necessary to achieve the desired accuracy. The encouraging results obtained from calculations on model structures highlight the great potential of application of structure modeling in theoretical study of POM. Structural modeling may not only reduce the computational cost of large POM species but also be able to take into account the external field effect arising from solvent molecules in solution or counterions in crystal.

The potential energy curves of low-lying electronic states of S2O.

Potential energy curves (PECs) of the symmetric and asymmetric bent S(2)O molecules are constructed using the configuration-based multireference second order perturbation theory and multireference configuration interaction with single and double excitations. Based on the PECs, the equilibrium structures of the ground state and several low-lying excited states, as well as the vertical and adiabatic transition energies, are obtained. Furthermore, avoided crossings and intersections displayed on the PECs are studied. The dissociation of states for the asymmetric bent S(2)O, especially the predissociative of the excited (~)C1A' state, is also discussed in detail. According to our calculations, the predissociation limit of (~)C1A' is found to be located in the vicinity of 2(6) or 2(5) (reckoning in the zero-point energy revision) S-S stretching vibration level, which is in good agreement with the available experimental data.

Detailed dynamics of the photodissociation of cyclobutane.

Semiclassical electron-radiation-ion dynamics simulations are reported for the photodissociation of cyclobutane into two molecules of ethylene. The results clearly show the formation of the tetramethylene intermediate diradical, with dissociation completed in approximately 400 fs. In addition, the potential energy surfaces of the electronic ground state and lowest excited-state were calculated at the complete-active-space self-consistent-field/multireference second-order perturbation theory (CASSCF/MRPT2) level with 6-31G* basis sets, along the reaction path determined by the dynamics simulations. There are well-defined energy minima and maxima in the intermediate state region. It is found that both C-C-C bond bending and rotation of the molecule (around the central C-C bond) have important roles in determining the features of the potential energy surfaces for the intermediate species. Finally, the simulations and potential energy surface calculations are applied together in a discussion of the full mechanism for cyclobutane photodissociation.