Small chromium-doped silicon clusters CrSin: structures, IR spectra, charge effect, magnetism and chirality.

A series of small chromium-doped silicon clusters CrSin with n = 3-10 in the cationic, neutral and anionic charge states were investigated using quantum chemical methods. The CrSin+ cations with n = 6-10 were produced in the gas phase and characterized by far-IR multiple photon dissociation (IR-MPD) spectroscopy. Good agreement between experimental spectra in the 200-600 cm-1 frequency range and those determined for the lowest-energy isomers by density functional theory calculations (B3P86/6-311+G(d)) provide a strong support for the geometrical assignments. An extensive structural comparison for the three different charge states shows that the structural growth mechanism inherently depends on the charge. While the structures of the cationic clusters are preferentially formed by addition of the Cr dopant to the corresponding pure silicon cluster, it favors substitution in both the neutral and anionic counterparts. The Si-Cr bonds of the studied CrSin+/0/- clusters are polar covalent. Apart from a basket-like Cr@Si9- and an endohedral Cr@Si10- cage, the Cr dopant takes an exohedral position and bears a large positive charge in the clusters. The exohedrally doped clusters also have a high spin density on Cr, manifesting the fact that the intrinsic magnetic moment of the transition metal dopant is well conserved. Three CrSin clusters have a pair of enantiomeric isomers in their ground state, namely the cationic n = 9 and the neutral and anionic n = 7. Those can be distinguished from each other by their electronic circular dichroism spectra, calculated using time-dependent density functional theory. Those enantiomers, being intrinsically chiral inorganic compounds, might be used as building blocks of optical-magnetic nanomaterials because of their high magnetic moments and ability to rotate the plane of polarization.

Importance of water and intramolecular interaction governs substantial blue shift of Csp2 -H stretching frequency in complexes between chalcogenoaldehydes and water.

Geometrical structure, stability and cooperativity, and contribution of hydrogen bonds to the stability of complexes between chalcogenoaldehydes and water were thoroughly investigated using quantum chemical methods. The stability of the complexes increases significantly when one or more H2O molecules are added to the binary system, whereas it decreases sharply going from O to S, Se, or Te substitution. The O-H⋯O H-bond is twice as stable as Csp2 -H⋯O and O-H⋯S/Se/Te H-bonds. It is found that a considerable blue-shift of Csp2 -H stretching frequency in the Csp2 -H⋯O H-bond is mainly determined by an addition of water into the complexes along with the low polarity of the Csp2 -H covalent bond in formaldehyde and acetaldehyde. The Csp2 -H stretching frequency shift as a function of net second hyperconjugative energy for the σ*(Csp2 -H) antibonding orbital is observed. Remarkably, a considerable Csp2 -H blue shift of 109 cm-1 has been reported for the first time. Upon the addition of H2O into the binary systems, halogenated complexes witness a decreasing magnitude of the Csp2 -H stretching frequency blue-shift in the Csp2 -H⋯O H-bond, whereas CH3-substituted complexes experience the opposite trend.

Unbinding ligands from SARS-CoV-2 Mpro via umbrella sampling simulations.

The umbrella sampling (US) simulation is demonstrated to be an efficient approach for determining the unbinding pathway and binding affinity to the SARS-CoV-2 Mpro of small molecule inhibitors. The accuracy of US is in the same range as the linear interaction energy (LIE) and fast pulling of ligand (FPL) methods. In detail, the correlation coefficient between US and experiments does not differ from FPL and is slightly smaller than LIE. The root mean square error of US simulations is smaller than that of LIE. Moreover, US is better than FPL and poorer than LIE in classifying SARS-CoV-2 Mpro inhibitors owing to the reciever operating characteristic-area under the curve analysis. Furthermore, the US simulations also provide detailed insights on unbinding pathways of ligands from the binding cleft of SARS-CoV-2 Mpro. The residues Cys44, Thr45, Ser46, Leu141, Asn142, Gly143, Glu166, Leu167, Pro168, Ala191, Gln192 and Ala193 probably play an important role in the ligand dissociation. Therefore, substitutions at these points may change the mechanism of binding of inhibitors to SARS-CoV-2 Mpro.

Theoretical Aspects of Nonconventional Hydrogen Bonds in the Complexes of Aldehydes and Hydrogen Chalcogenides.

Hydrogen bonds (H-bonds) in the complexes between aldehydes and hydrogen chalcogenides, XCHO...nH2Z with X = H, F, Cl, Br, and CH3, Z = O, S, Se, and Te, and n = 1,2, were investigated using high-level ab initio calculations. The Csp2-H...O H-bonds are found to be about twice as strong as the Csp2-H...S/Se/Te counterparts. Remarkably, the S/Se/Te-H...S/Se/Te H-bonds are 4.5 times as weak as the O-H...O ones. The addition of the second H2Z molecule into binary systems induces stronger complexes and causes a positive cooperative effect in ternary complexes. The blue shift of Csp2-H stretching frequency involving the Csp2-H...Z H-bond sharply increases when replacing one H atom in HCHO by a CH3 group. In contrast, when one H atom in HCHO is substituted with a halogen, the magnitude of blue-shifting of the Csp2-H...Z H-bond becomes smaller. The largest blue shift up to 92 cm-1 of Csp2-H stretching frequency in Csp2-H...O H-bond in CH3CHO...2H2O has rarely been observed and is much greater than that in the cases of the Csp2-H...S/Se/Te ones. The Csp2-H blue shift of Csp2-H...Z bonds in the halogenated aldehydes is converted into a red shift when H2O is replaced by a heavier analogue, such as H2S, H2Se, or H2Te. The stability and classification of nonconventional H-bonds including Csp2-H...Se/Te, Te-H...Te, and Se/Te-H...O have been established for the first time.

Transformation between Hexagonal Prism and Antiprism of the Singly and Doubly Cr-Doped Ge12 Clusters.

Structural transformation is a unique characteristic of atomic clusters, but it turns out very different from cluster to cluster. This theoretical study proves that the isomeric transformation between hexagonal prism and hexagonal antiprism is found for the doubly doped Cr2Ge12 cluster but not for singly doped CrGe12 cluster. We confirm that the ground state of CrGe12 is the distorted hexagonal prism C2h at the 3Bg triplet state instead of various shapes predicted in the previous studies. Upon comparison between the estimation at the B3P86/6-311+G(d) level of theory and the detachment energies measured by photoelectron spectroscopy, hexagonal antiprismatic shape is identified as the most stable isomer of the Cr2Ge12 cluster and it is easy to transform to the hexagonal prism-a less stable isomer by the rotation of the hexagonal rings. That is the first evidence for the structural transformation between a hexagonal prism and an antiprism of the germanium clusters, referring to the ability of Ge-based clusters in the formation of tubular geometry by doping Cr atoms. All the low-energy isomers of both Cr-doped germanium clusters have high magnetic moments. Interestingly, there is a tuning in magnetic properties of Cr2Ge12 from the ferromagnetism of the lowest-lying hexagonal antiprism to the ferrimagnetism of the higher-energy hexagonal prism. The stronger Cr-Cr bond and stronger interaction between the Cr2 moiety and the antiprism cage are accounted for by the higher stability of the hexagonal antiprismatic isomer.

Nature of the interaction between rare gas atoms and transition metal doped silicon clusters: the role of shielding effects.

Mass spectrometry experiments show an exceptionally weak bonding between Si7Mn(+) and rare gas atoms as compared to other exohedrally transition metal (TM) doped silicon clusters and other SinMn(+) (n = 5-10) sizes. The Si7Mn(+) cluster does not form Ar complexes and the observed fraction of Xe complexes is low. The interaction of two cluster series, SinMn(+) (n = 6-10) and Si7TM(+) (TM = Cr, Mn, Cu, and Zn), with Ar and Xe is investigated by density functional theory calculations. The cluster-rare gas binding is for all clusters, except Si7Mn(+) and Si7Zn(+), predominantly driven by short-range interaction between the TM dopant and the rare gas atoms. A high s-character electron density on the metal atoms in Si7Mn(+) and Si7Zn(+) shields the polarization toward the rare gas atoms and thereby hinders formation of short-range complexes. Overall, both Ar and Xe complexes are similar except that the larger polarizability of Xe leads to larger binding energies.

Structure assignment, electronic properties, and magnetism quenching of endohedrally doped neutral silicon clusters, Si(n)Co (n = 10-12).

The structures of neutral cobalt-doped silicon clusters have been assigned by a combined experimental and theoretical study. Size-selective infrared spectra of neutral Si(n)Co (n = 10-12) clusters are measured using a tunable IR-UV two-color ionization scheme. The experimental infrared spectra are compared with calculated spectra of low-energy structures predicted at the B3P86 level of theory. It is shown that the Si(n)Co (n = 10-12) clusters have endohedral caged structures, where the silicon frameworks prefer double-layered structures encapsulating the Co atom. Electronic structure analysis indicates that the clusters are stabilized by an ionic interaction between the Co dopant atom and the silicon cage due to the charge transfer from the silicon valence sp orbitals to the cobalt 3d orbitals. Strong hybridization between the Co dopant atom and the silicon host quenches the local magnetic moment on the encapsulated Co atom.

Structure, thermochemical properties, and growth sequence of aluminum-doped silicon clusters Si(n)Al(m) (n = 1-11, m = 1-2) and their anions.

A systematic examination of the aluminum doped silicon clusters, Si(n)Al(m) with n = 1-11 and m = 1-2, in both neutral and anionic states, is carried out using quantum chemical calculations. Lowest-energy equilibrium structures of the clusters considered are identified on the basis of G4 energies. High accuracy total atomization energies and thermochemical properties are determined for the first time using the G4 and CCSD(T)/CBS (coupled-cluster theory with complete basis set up to n = 3) methods. In each size, substitution of Si atoms at different positions of a corresponding pure silicon clusters by Al dopants invariably leads to a spectrum of distinct binary structures but having similar shape and comparable energy content. Such an energetic degeneracy persists in the larger cluster sizes, in particular for the anions. The equilibrium growth sequences for Al-doped Si clusters emerge as follows: (i) neutral singly doped Si(n)Al clusters favor Al atom substitution into a Si position in the structure of the corresponding cation Si(n+1)(+), whereas the anionic Si(n)Al(-) has one Si atom of the isoelectronic neutral Si(n+1) being substituted by the Al impurity; and (ii) for doubly doped Si(n)Al2(0/-) clusters, the neutrals have the shape of Si(n+1) counterparts in which one Al atom substitutes a Si atom and the other Al adds on an edge or a face of it, whereas the anions have both Al atoms substitute two Si atoms in the Si(n+2)(+) frameworks. The Al dopant also tends to avoid high coordination position.

The structures of neutral transition metal doped silicon clusters, Si(n)X (n = 6-9; X = V, Mn).

We present a combined experimental and theoretical investigation of small neutral vanadium and manganese doped silicon clusters Si(n)X (n = 6-9, X = V, Mn). These species are studied by infrared multiple photon dissociation and mass spectrometry. Structural identification is achieved by comparison of the experimental data with computed infrared spectra of low-lying isomers using density functional theory at the B3P86∕6-311+G(d) level. The assigned structures of the neutral vanadium and manganese doped silicon clusters are compared with their cationic counterparts. In general, the neutral and cationic Si(n)V(0,+) and Si(n)Mn(0,+) clusters have similar structures, although the position of the capping atoms depends for certain sizes on the charge state. The influence of the charge state on the electronic properties of the clusters is also investigated by analysis of the density of states, the shapes of the molecular orbitals, and NBO charge analysis of the dopant atom.

Mn@Si14+: a singlet fullerene-like endohedrally doped silicon cluster.

The electronic structure of Mn@Si14(+) is determined using DFT and CASPT2/CASSCF(14,15) computations with large basis sets. The endohedrally Mn-doped Si cationic cluster has a D3h fullerene-like structure featuring a closed-shell singlet ground state with a singlet-triplet gap of ~1 eV. A strong stabilizing interaction occurs between the 3d(Mn) and the 2D-shell(Si14) orbitals, and a large amount of charge is transferred from the Si14 cage to the Mn dopant. The 3d(Mn) orbitals are filled by encapsulation, and the magnetic moment of Mn is completely quenched. Full occupation of [2S, 2P, 2D] shell orbitals by 18 delocalized electrons confers the doped Mn@Si14(+) cluster a spherically aromatic character.

High magnetic moments in manganese-doped silicon clusters.

We report on the structural, electronic, and magnetic properties of manganese-doped silicon clusters cations, Si(n)Mn(+) with n=6-10, 12-14, and 16, using mass spectrometry and infrared spectroscopy in combination with density functional theory computations. This combined experimental and theoretical study allows several structures to be identified. All the exohedral Si(n)Mn(+) (n=6-10) clusters are found to be substitutive derivatives of the bare Si(n+1)(+) cations, while the endohedral Si(n)Mn(+) (n=12-14 and 16) clusters adopt fullerene-like structures. The hybrid B3P86 functional is shown to be appropriate in predicting the ground electronic states of the clusters and in reproducing their infrared spectra. The clusters turn out to have high magnetic moments localized on Mn. In particular the Mn atoms in the exohedral Si(n)Mn(+) (n=6-10) clusters have local magnetic moments of 4 µ(B) or 6 µ(B) and can be considered as magnetic copies of the silicon atoms. Opposed to other 3d transition-metal dopants, the local magnetic moment of the Mn atom is not completely quenched when encapsulated in a silicon cage.

Ionization energies and structures of lithium doped silicon clusters.

We report on a combined experimental and theoretical study of the ionization energies and structures of small lithium doped silicon clusters, SinLim with n = 5-11 and m = 3-6. Photoionization efficiency curves are measured in the 4.68-6.24 eV range and subsequently compared with calculated values of both vertical and adiabatic ionization energies for the lowest energy isomers obtained using density functional theory at the B3LYP/6-311+G(d) level. The evolution of the cluster geometries and ionization energies is studied as a function of the number of silicon and lithium atoms along the SinLi3 (n = 5-11) and Si8Lim (m = 1-6) series, respectively. For most studied sizes good agreement is found between the experimental and the calculated ionization energies for the lowest-energy isomer. In the SinLi3 (n = 5-11) series, positively charged lithium atoms surround a negatively charged silicon framework and mainly act as electron donors. Upon sequential lithium addition along the Si8Lim (m = 1-6) series, the Si8 framework deforms from a rhombic (m = 0, 1) over a tetracapped tetragon (m = 1-4) to a square antiprism (m = 4-6) structure. Subsequent addition of lithium implies the addition of excess electrons to the silicon framework, which is reflected in a decrease of the ionization energy with increasing lithium content. This decrease is non-monotonous and odd-even alternations, reflecting the higher stability of clusters with an even number of electrons, are observed. In addition, post-threshold features in the experimental photoionization efficiency curves of SinLi3 (n = 8-11) may be related to the computed density of states of the corresponding lowest energy isomers.

Singly and doubly lithium doped silicon clusters: geometrical and electronic structures and ionization energies.

The geometric structures of neutral and cationic Si(n)Li(m)(0/+) clusters with n = 2-11 and m = 1, 2 are investigated using combined experimental and computational methods. The adiabatic ionization energy and vertical ionization energy (VIE) of Si(n)Li(m) clusters are determined using quantum chemical methods (B3LYP/6-311+G(d), G3B3, and CCSD(T)/aug-cc-pVxZ with x = D,T), whereas experimental values are derived from threshold photoionization experiments in the 4.68-6.24 eV range. Among the investigated cluster sizes, only Si(6)Li(2), Si(7)Li, Si(10)Li, and Si(11)Li have ionization thresholds below 6.24 eV and could be measured accurately. The ionization threshold and VIE obtained from the experimental photoionization efficiency curves agree well with the computed values. The growth mechanism of the lithium doped silicon clusters follows some simple rules: (1) neutral singly doped Si(n)Li clusters favor the Li atom addition on an edge or a face of the structure of the corresponding Si(n)(-) anion, while the cationic Si(n)Li(+) binds with one Si atom of the bare Si(n) cluster or adds on one of its edges, and (2) for doubly doped Si(n)Li(2)(0/+) clusters, the neutrals have the shape of the Si(n+1) counterparts with an additional Li atom added on an edge or a face of it, while the cations have both Li atoms added on edges or faces of the Si(n)(-) clusters.

Electronic structures, vibrational and thermochemical properties of neutral and charged niobium clusters Nb(n), n = 7-12.

Geometric and electronic structures, vibrational properties, and relative stabilities of niobium clusters Nb(n), n = 7-12, are studied using both DFT (BPW91 and M06 functionals) and CCSD(T) calculations with the cc-pVnZ-PP basis set. In each cluster, various lower-lying states are very close in energy in such a way that the ground state cannot be unambiguously established by DFT computations. Nb clusters tend to prefer the lowest possible spin state as the ground state, except for Nb(12) ((3)A(g)). The optimal structure of the cluster at a certain size does not simply grow from that of the smaller one by adding an atom randomly. Instead, the Nb clusters prefer a close-packed growth behavior. Nb(10) has a spherically aromatic character, high chemical hardness and large HOMO-LUMO gap. Electron affinities, ionization energies, binding energy per atom, and the stepwise dissociation energies are evaluated. Energetic properties exhibit odd-even oscillations. Comparison with experimental values shows that both BPW91 and M06 functionals are reliable in predicting the EA and IE values, but the BPW91 is deficient in predicting the binding and dissociation energies. We re-examine in particular the experimental far IR spectra previously recorded using the IR-MPD and free electron laser spectrometric techniques and propose novel assignments for Nb(7) and Nb(9) systems. The IR spectra of the anions are also predicted.

Experimental detection and theoretical characterization of germanium-doped lithium clusters Li(n)Ge (n = 1-7).

We report a combined experimental and quantum chemical study of the small neutral and cationic germanium-doped lithium clusters Li(n)Ge(0,+) (n = 1-7). The clusters were detected by time-of-flight mass spectrometry after laser vaporization and ionization. The molecular geometries and electronic structures of the clusters were investigated using quantum chemical calculations at the DFT/B3LYP and CCSD(T) levels with the aug-cc-pVnZ basis sets. While Li3Ge(0,+) and Li4Ge+ prefer planar structures, the clusters from Li4Ge to Li7Ge and the corresponding cations (except Li4Ge+) exhibit nonplanar forms. Clusters having from 4 to 6 valence electrons prefer high spin structures, and low spin ground states are derived for the others because valence electron configurations are formed by filling the electron shells 1s/1p/2s/2p based on Pauli's and Hund's rules. Odd-even alternation is observed for both neutral and cationic clusters. Because of the closed electronic shells, the 8- and 10-electron systems are more stable than the others, and the 8-electron species (Li4Ge, Li5Ge+) are more favored than the 10-electron ones (Li6Ge, Li7Ge+). This behavior for Ge is different from C in their doped Li clusters, which can be attributed to the difference in atomic radii. The averaged binding energy plot for neutrals tends to increase slowly with the increasing number of Li atoms, while the same plot for cations shows a maximum at Li5Ge+, which is in good agreement with the mass spectrometry experiment. Atom-in-molecules (AIM) analysis suggests that Li atoms do not bond to one another but through Ge or pseudoatoms, and an essentially ionic character can be attributed to the cluster chemical bonds. An interesting finding is that the larger clusters have the smallest adiabatic ionization energies known so far (IEa approximately 3.5 eV).

Thermochemistry and electronic structure of small boron and boron oxide clusters and their anions.

Thermochemical properties of a set of small boron (B(n)) and boron oxide (B(n)O(m)) clusters, with n = 1-4 and m = 0-3, their anions, and the B(4)(2-) dianion, were calculated by using coupled-cluster theory CCSD(T) calculations with the aug-cc-pVnZ (n = D, T, Q, 5) basis sets extrapolated to the complete basis set limit with additional corrections. Enthalpies of formation, bond dissociation energies, singlet-triplet or doublet-quartet separation gaps, adiabatic electron affinities (EA), and both vertical electron attachment and detachment energies were evaluated. The predicted heats of formation show agreement close to the error bars of the literature results for boron oxides with the largest error for OBO. Our calculated adiabatic EAs are in good agreement with recent experiments: B (calc, 0.26 eV; exptl, 0.28 eV), B(2) (1.95, 1.80), B(3) (2.88, 2.820 +/- 0.020), B(4) (1.68, 1.60 +/- 0.10), BO (2.50, 2.51), BO(2) (4.48, 4.51), BOB (0.07), B(2)O(2) (0.37), B(3)O (2.05), B(3)O(2) (2.94, 2.94), B(4)O (2.58), and B(4)O(2) (3.14, 3.160 +/- 0.015). The BO bond is strong, so this moiety is maintained in most of the clusters. Thermochemical parameters of clusters are not linearly additive with respect to the number of B atoms. The EA tends to be larger in the dioxides. The growth mechanism of small boron oxides should be determined by a number of factors: (i) formation of BO bonds, (ii) when possible, formation of a cyclic B(3) or B(4), and (iii) combination of a boron cycle and a BO bond. When these factors compete, the strength of the BO bonds tends to compensate the destabilization arising from a loss of binding in the cyclic boron clusters, in such a way that a linear boron oxide prevails. When the B(2) moiety is present in these linear clusters, the oxide derivatives prefer a high spin state.

Electronic structure of germanium monohydrides Ge(n)H, n = 1-3.

Quantum chemical calculations were applied to investigate the electronic structure of germanium hydrides, Ge(n)H (n = 1, 2, 3), their cations, and anions. Computations using a multiconfigurational quasi-degenerate perturbation approach (MCQDPT2) based on complete active space wave functions (CASSCF), multireference perturbation theory (MRMP2), and density functional theory reveal that Ge(2)H has a (2)B(1) ground state with a doublet-quartet gap of approximately 39 kcal/mol. A quasidegenerate (2)A(1) state has been derived to be 2 kcal/mol above the ground state (MCQDPT2/aug-cc-pVTZ). In the case of the cation Ge(3)H(+) and anion Ge(3)H(-), singlet low-lying electronic states are derived, that is, (1)A' and (1)A(1), respectively. The singlet-triplet energy gap is estimated to 6 kcal/mol for the cation. An "Atoms in Molecules" (AIM) analysis shows a certain positive charge on the Ge(n) (n = 1, 2, 3) unit in its hydrides, in accordance with the NBO analysis. The topologies of the electron density of the germanium hydrides are different from that of the lithium-doped counterparts. On the basis of our electron localization function (ELF) analysis, the Ge-H bond in Ge(2)H is characterized as a three-center-two-electron bond. Some key thermochemical parameters of Ge(n)H have also been derived.

Carboxyl-functionalized task-specific ionic liquids for solubilizing metal oxides.

Imidazolium, pyridinium, pyrrolidinium, piperidinium, morpholinium, and quaternary ammonium bis(trifluoromethylsulfonyl)imide salts were functionalized with a carboxyl group. These ionic liquids are useful for the selective dissolution of metal oxides and hydroxides. Although these hydrophobic ionic liquids are immiscible with water at room temperature, several of them form a single phase with water at elevated temperatures. Phase separation occurs upon cooling. This thermomorphic behavior has been investigated by (1)H NMR, and it was found that it can be attributed to the temperature-dependent hydration and hydrogen-bond formation of the ionic liquid components. The crystal structures of four ionic liquids and five metal complexes have been determined.

Ion-molecule reactions involving methyl isocyanide and methyl cyanide.

Ion-molecule reactions involving methyl isocyanide and methyl cyanide have been performed in a new rf-only hexapole collision cell inserted in a large-scale tandem mass spectrometer. Beside protonation processes, N-methyl cyanogen ions (CH(3)N(+)CCN) and 1-methyleneiminium-1- ethylenium ions (CH(2)CN(+)CH(2)) have been produced in high yield and fully characterized by high-energy collisional activation. The unimolecular chemistry of the molecular ions of caffeine (1,3,7-trimethyl xanthine) has been revisited on the basis of these new results.