Plasmapause surface wave oscillates the magnetosphere and diffuse aurora.

Energy circulation in geospace lies at the heart of space weather research. In the inner magnetosphere, the steep plasmapause boundary separates the cold dense plasmasphere, which corotates with the planet, from the hot ring current/plasma sheet outside. Theoretical studies suggested that plasmapause surface waves related to the sharp inhomogeneity exist and act as a source of geomagnetic pulsations, but direct evidence of the waves and their role in magnetospheric dynamics have not yet been detected. Here, we show direct observations of a plasmapause surface wave and its impacts during a geomagnetic storm using multi-satellite and ground-based measurements. The wave oscillates the plasmapause in the afternoon-dusk sector, triggers sawtooth auroral displays, and drives outward-propagating ultra-low frequency waves. We also show that the surface-wave-driven sawtooth auroras occurred in more than 90% of geomagnetic storms during 2014-2018, indicating that they are a systematic and crucial process in driving space energy dissipation.

Catalytic coupling reaction mechanism of 4-nitrobenzenethiol on silver clusters: a density functional theoretical study.

The catalytic coupling reaction mechanism of the transformation from 4-nitrobenzenethiol (4-NBT) to 4,4'-dimercaptoazobenzene (4,4'-DMAB) on a silver cluster was studied by density functional theory. Reactants, intermediates, transition states and products were optimized with the B3LYP method using the 6-311 + G(d,p) basis set (Ag using the pseudo potential basis set of LanL2DZ). Transition states and intermediates were confirmed by the corresponding vibration analysis and intrinsic reaction coordinates (IRC). Consistent with literature reports, the key point of the transformation from 4-NBT absorbed on the surface of Ag5 clusters to 4,4'-DMAB is the elimination of two O atoms on the amino group. Meanwhile, the catalytic coupling reaction of 4-nitrobenzenethiol on a silver cluster is easy to carry out under irradiation. The possibility of "inter system channeling" (ISC) between different potential energy surfaces in the coupling reaction of 4-NBT is further discussed. The irradiation has an auxiliary catalytic effect on the coupling reaction. Our research results can explain the observed experimental phenomena. Graphical abstract Catalytic coupling reaction mechanism of the transformation from 4-nitrothiophenol (4-NBT) to 4,4'-dimercaptoazobenzene (4,4'-DMAB) on silver clusters studied by density functional theory.

Communication: Competition between π···π interaction and halogen bond in solution: a combined 13C NMR and density functional theory study.

Competition between π···π interaction and halogen bond in solution has been investigated by using carbon nuclear magnetic resonance spectroscopy ((13)C NMR) combined with density functional theory calculation. Both experimental and theoretical results clearly show that there are no C-Cl···π or C-Br···π halogen bonds and only the π···π interactions exist in the binary liquid mixtures of C(6)D(6) with C(6)F(5)Cl and C(6)F(5)Br, respectively. The case is totally different for the binary liquid mixtures of C(6)D(6) with C(6)F(5)I in which the C-I···π halogen bonds not the π···π interactions are present. The important role of entropy in the competition between π···π interaction and halogen bond in solution was also discussed.

Structural competition between halogen bonds and lone-pair···π interactions in solution.

Structural competition between halogen bonds and lone-pair···π interactions in solution is studied using (13)C NMR combined with density functional theory calculations. Among the halogen bonds considered, only the iodine bonds and a few bromine bonds are strong enough to compete successfully with the lone-pair···π interactions.

Effects of the position and manner of hydration on the stability of solvated N-methylacetamides and the strength of binding between N-methylacetamide and water clusters: a computational study.

This work mainly studies the effects of the position (there are two possible hydrated sites) and the manner (i.e., whether water acts as a proton donor or acceptor) of hydration by various numbers of water molecules on the stability of 14 solvated N-methylacetamide structures, NMA-(H(2)O)( n ) (n = 1-3), as well as the binding strength between the NMA and the water cluster, using molecular dynamics (MD) and B3LYP methods. Natural bond orbital (NBO) analysis is used to explore the origin of these effects. Some novel observations are obtained from the work. Our results show that monohydration at the carbonyl site favors stability and binding strength compared to monohydration at the amino site. Similarly, the preferred hydration at the carbonyl site is observed for dihydrated NMAs when the second water is added as a proton donor to the C=O group or the first water is H-bonded to the C=O group. However, unfavorable hydration at the C=O site occurs if the second water acts as a proton acceptor. Trihydration by a ring cluster of three water molecules at either the carbonyl site or the amino one yields relatively stable complexes, but significantly disfavors binding strength. The other trihydrated NMAs show similar behavior to dihydrated NMAs. In addition, our results show that the C=O and N-H frequencies can still be utilized to examine the H-bond effects of the water cluster.

On the correlation between bond-length change and vibrational frequency shift in halogen-bonded complexes.

The C-Hal (Hal = Cl, Br, or I) bond-length change and the corresponding vibrational frequency shift of the C-Hal stretch upon the C-Hal···Y (Y is the electron donor) halogen bond formation have been determined by using density functional theory computations. Plots of the C-Hal bond-length change versus the corresponding vibrational frequency shift of the C-Hal stretch all give straight lines. The coefficients of determination range from 0.94366 to 0.99219, showing that the correlation between the C-Hal bond-length change and the corresponding frequency shift is very good in the halogen-bonded complexes. The possible effects of vibrational coupling, computational method, and anharmonicity on the bond-length change-frequency shift correlation are discussed in detail.

Theoretical study on the ring-opening isomerization reaction mechanism of the ring isomers of N8H8.

Ring-opening isomerization from ring-shaped isomers to chain-shaped isomers of N(8)H(8) has been studied by a density function B3LYP method at 6-311+ +G** level. 20 ring-shaped isomers have been found to be able to transform into chain-shaped isomers, with 20 possible transition states got by ring-opening structure optimization. Furthermore, the ring-openings have been found in the longer N-N single bond by analyzing the length change of N-N bond of ring-shaped isomers in ring-opening processes. In addition, with the activation energies in ring-opening processes, the differences of the activation energies in isomerization between the isomers have been found according to the classification of rings. The activation energies in ring-opening isomerization of six-membered ring-shaped isomers are higher than that of the four-membered ring-shaped isomers. It indicates that six-membered ring-shaped isomers difficult in ring-opening in the isomerization are the steadiest ring-shaped isomers of N(8)H(8) while four-membered ring-shaped isomers easy in ring-opening are the most unstable.

Hydrogen bond and halogen bond inside the carbon nanotube.

The hydrogen bond and halogen bond inside the open-ended single-walled carbon nanotubes have been investigated theoretically employing the newly developed density functional M06 with the suitable basis set and the natural bond orbital analysis. Comparing with the hydrogen or halogen bond in the gas phase, we find that the strength of the hydrogen or halogen bond inside the carbon nanotube will become weaker if there is a larger intramolecular electron-density transfer from the electron-rich region of the hydrogen or halogen atom donor to the antibonding orbital of the X-H or X-Hal bond involved in the formation of the hydrogen or halogen bond and will become stronger if there is a larger intermolecular electron-density transfer from the electron-rich region of the hydrogen or halogen atom acceptor to the antibonding orbital of the X-H or X-Hal bond. According to the analysis of the molecular electrostatic potential of the carbon nanotube, the driving force for the electron-density transfer is found to be the negative electric field formed in the carbon nanotube inner phase. Our results also show that the X-H bond involved in the formation of the hydrogen bond and the X-Hal bond involved in the formation of the halogen bond are all elongated when encapsulating the hydrogen bond and halogen bond within the carbon nanotube, so the carbon nanotube confinement may change the blue-shifting hydrogen bond and the blue-shifting halogen bond into the red-shifting hydrogen bond and the red-shifting halogen bond. The possibility to replace the all electron nanotube-confined calculation by the simple polarizable continuum model is also evaluated.

Discovery of singlet diradicals: theoretical study on the cage species C14N12-H6 and its six derivatives.

In this work, the geometries, harmonic vibrational frequencies, and high-energy density material (HEDM) properties of a novel species and its six derivatives with the general formula C14N12-R6 (R = H, OH, F, CN, N3, NH2, and NO2) have been investigated at the restricted and unrestricted B3LYP/cc-pVDZ levels of theory. Natural bond orbital (NBO), natural orbital (NO), and atoms in molecules (AIM) analyses are applied to examine their electronic topologies. It is found that for the four species of R = H, CN, N3, and NO2, (1) there exist high LUMO occupation numbers, (2) there is considerable spin density congregated on the two central carbon atoms, (3) there exists through space interaction (or intramolecular interaction, which is one of the stabilizing factors of a diradicaloid) between the two central carbon atoms, (4) the distance (about 3 A) between the two central carbon atoms (as the apexes of two trigonal pyramids with their bases facing each other) is suitable and favorable for diradical formation. All the results support that these four species are diradicals or diradicaloids. Furthermore, the appreciable singlet-triplet energy gaps indicate that these four diradicals tend to have a singlet ground state. There is a moderate HOMO-LUMO gap (on the order of 1.5 to 2.1 eV) for these four species. These four singlet diradicals may be novel organic semiconductor materials or nonlinear optical materials. On the other hand, the remaining three species, with R = OH, F, and NH2, are not diradicaloids.

Theoretical investigation on carbon-centered tri-s-tetrazine and its 10 derivatives.

A novel species, carbon-centered tri-s-tetrazine (C(4)N(9)H(3)), and its 10 derivatives (C(4)N(9)R(3), where R=OH, F, CN, N(3), NH(2), NO(2), N=NH, N(2)H(3), C triple bond CH, and CH=CH(2)) have been studied computationally. Density functional theory (DFT) has been used to study the geometries, electronic structure, harmonic vibrational frequencies, ionization energies of the 11 compounds at the restricted (for neutrals) and the unrestricted (for cations) B3LYP/cc-pVDZ level of theory. Atoms in molecule (AIM) and natural bond orbital (NBO) analyses have been used to obtain the bonding properties. Valence bond (VB) theory is applied to explain the unusual pyramidal structure around the carbon-center and electron arrangements of orbitals. We found: (1) All the species possess novel bonding features and geometrical structures. The atoms on the periphery of each species are sp(2) hybridized. Each of these atoms offers an orbital to form an extensive conjugation system (12)pi(15) (a pi system consisting of 12 centers and 15 electrons). The central carbon atom C13 is sp(3) hybridized, which makes the non-planar molecule shape like a straw-hat. Atom C13 also participates in the conjugated pi system with its sp(3) hybridized orbital, thus forming an extensive (13)pi(16) conjugate pi system covering the whole C(4)N(9) framework. (2) The change of charge on C13 is the largest among all the atoms when the species is ionized and the atomic charges are redistributed. In other words, C13 is the attack center for electrophilic agents. Thus, the species is carbanion-like. (3) All the species have low ionization energies (IEs). The electron ionized mainly comes from C13. They may have wide applications in organic chemistry, in organometallic chemistry and in alkyl lithium chemistry once they are synthesized.

Theoretical study on the cylinder-shaped N78 cage.

Recent theoretical studies have suggested that the stabilizing factors for large nitrogen cages tend to favor more five-membered rings, more three-membered rings and cylindrical structure with large numbers of layers. Further studies of relative stability of the all-nitrogen molecule have prompted to figure out what brings about the stabilizing factors. Herein, the cylinder-shaped molecule of N(78) (D(3h)) has been studied in detail. The geometry and energies are examined at B3LYP/cc-pVDZ and single point energy calculations at MP2/cc-pVDZ are carried out for the purposes of determining relative thermodynamic stability. NBO analysis and AIM analysis are applied to investigate the bonding properties of the cage molecule. The major result of this study is the identification of intra-molecular interactions, whether it is at B3LYP/cc-pVDZ or at MP2/cc-pVDZ, as the dominant stabilizing factor for the large all-nitrogen cage. The length of the cylinder-shaped molecule is about 2.5nm. N(78) (D(3h)) might be one novel nanomaterial which is environment-friendly and as a beeline nanotube or a beeline "nano-bar", it is expected to impact a wide range of applications.

What makes the cylinder-shaped N72 cage stable?

Recent theoretical studies have suggested that the stabilizing factors for large nitrogen cages tend to favor more five-membered rings, more three-membered rings, and cylindrical structures with large numbers of layers. One of the major issues in this study of the all-nitrogen molecule is the determination of what brings about the stabilizing factors. Herein, the cylinder-shaped molecule of N72 (D3d) has been studied in detail. The geometry and energies are examined at B3LYP/cc-pVDZ, and single-point energy calculations at MP2/cc-pVDZ are carried out for the purposes of determining relative thermodynamic stability. Natural bond order (NBO) analysis and atoms in molecules (AIM) analysis are applied to investigate the bonding properties of the cage molecule. The major result of this study is the identification of intramolecular interactions, whether it is at B3LYP/cc-pVDZ or at MP2/cc-pVDZ, as the dominant stabilizing factor for the large all-nitrogen cage. The length of the cylinder-shaped molecule is about 2.2 nm. N72 (D3d) might be one novel nanomaterial which is environment friendly, and as a beeline nanotube or a beeline "nano-bar", it is expected to impact a wide range of applications.

Theoretical investigation on the replacement of CH groups by N atoms in caged structure (CH)8.

A molecular design was performed for the caged molecule (CH)8: the replacement of CH groups by N atoms to increase the content of N as well as reduce the content of H. A series of caged molecules were obtained: (CH)xN(8-x) (0 < or = n < or = 8). The studied aspects are as follows: (i) molecular geometries and electronic structures, (ii) the analysis of the electronic structure using natural bond orbital (NBO) and atoms in molecules (AIM), and (iii) some physicochemical properties of studied molecules, such as the dipole moments, IR vibrational spectra, NMR chemical shifts, heats of formation, and relative specific impulses, were provided. Our studies show that these molecules should be a kind of potential and novel energetic material. Our work provides some useful information for the experimental study of these molecules. The effect of the substitution of N atoms for CH groups on the properties of this kind of caged molecule is presented.

Theoretical study on "multilayer" nitrogen cages.

The relative stabilities of nonisomers are investigated. Twenty-two species of nitrogen cage molecules N(2n) (N6 (D(3h)), N8 (Oh), N10 (D(5h)), N12 (D(6h)), N12 (D(3d)), N16 (D(4d)), N18 (D(3h)), N20 (Ih), N24 (D(3d)), N24 (D(4h)), N24 (D(6d)), N30 (D(3h)), N30 (D(5h)), N32 (D(4d)), N36 (D(3d)), N40 (D(4h)), N42 (D(3h)), N48 (D(4d)), N48 (D(3d)), N54 (D(3h)), N56 (D(4h)), and N60 (D(3d))), which are divided into four sets, have been studied in detail. The geometries and varieties of energies are examined extensively, and NBO analysis and AIM analysis are applied to investigate the bonding properties of the cage molecules. The introducing of the concept of "layer" can well assist in explaining why one nonisomer molecule is more stable than another one. The results show that the lengths of bonds, on both sides of which are five-membered rings (referred to as pentagons), are the shortest and the orbital energies are the lowest. The nonlocalized electron numbers of orbitals, on at least one side of which is a triangle, are the greatest. Pentagons play a major role in the stability of a cage molecule, and the three-membered rings (referred to as triangles) play the second one. The layers in nitrogen cage molecules also contribute to the relative stabilities.

Modeling of hydrogen bonds in monohydrated 2,4-dithiothymine: an ab initio and AIM study.

Twelve tautomers of 2,4-dithiothymine are calculated at the MP2/6-31+G(d) level, and the most stable one is referred to the di-keto form (P12). Then four H-bonded complexes between P12 and water are optimized at the MP2/6-31+G(d) level of theory. The calculation of vibrational frequencies and natural bond orbital analysis are also carried out at the same level to investigate the hydrogen bonds involved in all the systems. Within all the four complexes, three types of hydrogen bonds are formed, in which the O-H...S and N-H...O bonds are the normal bonds with the X-H bond elongation and red shift of the corresponding stretch frequencies, while the C-H...O interaction is an improper, blue-shifting hydrogen bond accompanied with the contraction of the C-H bond and a blue shift of the C-H stretch frequency. The topological properties are investigated with the atoms-in-molecules (AIM) theory. The NMR chemical shielding for the isolated and the four monohydrated 2,4-dithiothymine are calculated using the "gauge-including atomic orbital" (GIAO) method. The 1H chemical shifts are influenced by the formation of hydrogen bonds.

Theoretical Studies on the Nonlinear Optical Properties of Octupolar Tri-s-triazines.

The first-, second-, and third-order static and frequency-dependent polarizabilities of a series of octupolar tri-s-triazines have been investigated by using the ab initio coupled perturbed Hartree-Fock (CPHF) method. Effects of substitution have also been considered. The results show that α, ß, and γ values for octupolar tri-s-triazines are much larger than those for s-triazine in both static and frequency-dependent cases. Attaching groups containing π systems such as azide and ethenyl to the tri-s-triazine molecule results in a significant increase of first-, second-, and third-order polarizabilities. Our calculations suggest that the octupolar tri-s-triazines may be prospective candidates for nonlinear optical materials.

Anion-tri-s-triazine bonding: a case for anion recognition.

An ab initio study of the possible interaction between several anions (F(-), Cl(-), N(3)(-), N(4)(-), and N(5)(-)) and tri-s-triazine molecule, an electron-deficient aromatic ring, has been carried out at the B3LYP and MP2 levels of theory. Minima are located corresponding to hydrogen bonding, pi-pi stacking, and reactive complexes. This novel mode of bonding suggests the development of new cyclophane-type receptors for the recognition of anions.

Theoretical study on the bromomethane-water 1:2 complexes.

Bromomethane-water 1:2 complexes have been theoretically studied to reveal the role of hydrogen bond and halogen bond in the formation of different aggregations. Four stable structures exist on the potential energy surface of the CH3Br(H2O)2 complex. The bromine atom acts mainly as proton acceptor in the four studied structures. It is also capable of participating in the formation of the halogen bond. The properties and characteristics of the hydrogen bond and the halogen bond are investigated employing several different quantum chemical analysis methods. Cooperative effects for the pure hydrogen bonds or the mixed hydrogen bonds with halogen bonds and the possibility of describing cooperative effects in terms of the topological analysis of the electronic density or the charge-transfer stabilization energy are discussed in detail. An atoms-in-molecules study of the hydrogen bond or the halogen bond in the bromomethane-water 1:2 complexes suggests that the electronic density topology of the hydrogen bond or the halogen bond is insensitive to the cooperative effect. The charge-transfer stabilization energy is proportional to the cooperative effect, which indicates the donor-acceptor electron density transfer to be mainly responsible for the trimer nonadditive effect.