Natural bond orbital analysis of some para-substituted N-nitrosoacetanilide biological molecules

Theoretical study of several para-substituted N-nitrosoacetanilide biological molecules has been performed using density functional B3LYP method with 6-31G(d,p) basis set. Geometries obtained from DFT calculation were used to perform natural bond orbital analysis. The p characters of two nitrogen natural hybrid orbital (NHO) σ _N3–N2 bond orbitals increase with increasing σ _p values of the para substituent group on the benzene, which results in a lengthening of the N₃–N₂ bond. The p characters of oxygen NHO σ _O1–N2 and nitrogen NHO σ _O1–N2 bond orbitals decrease with increasing σ _p values of the para substituent group on the benzene, which results in a shortening of the N₂=O₁ bond. It is also noted that decreased occupancy of the localized σ _N3–N2 orbital in the idealized Lewis structure, or increased occupancy of s_N3-N2^* \sigma_{\rm N3-N2}^{\ast} of the non-Lewis orbital, and their subsequent impact on molecular stability and geometry (bond lengths) are also related with the resulting p character of the corresponding nitrogen NHO of σ _N3–N2 bond orbital.     

Valence-bond studies of AH2 molecules

Minimal Slater basis set calculations are reported for H₂S. The calculations used both natural and hybrid atomic orbitals. The calculations were performed at H-S-H bond angles of 90 °, 92.2 ° and 95 °. The results are compared with similar calculations on H₂O and with calculations using the molecular orbital approximation. The only definite trend found in going from H₂O to H₂S is that the importance of the SH⁺H^– structure decreases. Changes in the relative importance of covalent and ionic structures depend upon which measure of importance is used. Calculations using a set of orthogonal hybrid orbitals again find the hybrid orbitals exhibiting non-perfect following behaviour with the hybrids remaining at about the equilibrium bond angle. Localized molecular orbitals were found to move in the opposite direction to the change in the H-S-H bond angle.     

Valence bond studies of AH2 molecules

Minimal basis set (STO) molecular orbital and valence-bond calculations are reported for the³ B ₁ and¹ A ₁ states of CH₂. The open-shell molecular orbital calculations used the Roothaan formulation. The valence-bond calculations used the Prosser-Hagstrom biorthogonalisation technique to evaluate the cofactors required in using Löwdin's formulae. Optimisation of geometry and orbital exponents in the molecular orbital calculation on the³ B ₁ state gave a geometry of R_C-H=2.11 a.u. and H-C-H=123.2 °. The energy obtained was ?38.8355 a.u. The molecular orbital and valencebond calculations are compared. In the valence-bond calculations the variation with bond-length and bond-angle of the configuration energies was studied. Valence bond “build-up” studies are also reported. Valence-bond calculations using hybrid orbitals instead of natural atomic orbitals showed that the perfect-pairing approximation is not as good for CH₂ as BeH₂. The nature of the lone-pair and bonding orbitals is found to be significantly different between the³ B ₁ and¹ A ₁ states. In the³ B ₁ state the 2s and 2p orbitals are fairly equally mixed between both types of orbital. However in the¹ A ₁ state the bonding orbitals have mainly 2p character and the lone pair orbitals have mainly 2s character. As was found for H₂O, the bonding hybrid orbitals do not follow the hydrogen nuclei as the bond angle varies but continue to point approximately in their equilibrium directions.     

Laser Sculpting of Atomic sp,sp2, and sp3 Hybrid Orbitals

Atomic sp, sp², and sp³ hybrid orbitals were introduced by Linus Pauling to explain the nature of the chemical bond. Quantum dynamics simulations show that they can be sculpted by means of a selective series of coherent laser pulses, starting from the 1s orbital of the hydrogen atom. Laser hybridization generates atoms with state‐selective electric dipoles, opening up new possibilities for the study of chemical reaction dynamics and heterogeneous catalysis.     

Transition metal complexes enslaved in the supercages of zeolite-Y: DFT investigation and catalytic significance

A series of zeolite-Y encapsulated hybrid catalysts, [M(STCH)·xH₂O]-Y have been prepared by encapsulating Schiff base complexes [where M?=?Mn(II), Fe(II), Co(II), Ni(II); (x?=?3) and Cu(II); (x?=?1); H₂STCH?=?salicylaldehyde thiophene-2-carboxylic hydrazone] in zeolite-Y matrix by flexible ligand method. These hybrid materials have been characterized by various physico-chemical techniques such as ICP-OES, elemental analyses, (FT-IR and electronic) spectral studies, BET, scanning electron micrographs, thermal analysis and X-ray powder diffraction patterns. X-ray powder diffraction analysis reveals that the structural integrity of the mother zeolite in the hybrid material remained intact upon immobilization of the complex. Density functional theory is employed to calculate the relaxed structure, bond angle, bond distance, dihedral angle, difference of highest occupied molecular orbital and lowest unoccupied molecular orbital energies gap and electronic density of states of ligand and their neat transition metal complexes. The hybrid materials are active catalysts for the hydroxylation of phenol using hydrogen peroxide (30% H₂O₂) as an oxidant in order to selectively synthesize catechol or hydroquinone, amongst them [Cu(STCH)·H₂O]-Y shown the highest % of selectivity towards catechol (81.3%).     

复合物HNO···H2O2内N-H···O蓝移氢键的理论研究

A theoretical study on the blue-shifted H-bond N-H…O and red-shifted H-bond O-H…O in the complexHNO…H_2O_2 was conducted by employment of both standard and counterpoise-corrected methods to calculate thegeometric structures and vibrational frequencies at the MP2/6-31G(d),MP2/6-31 G(d,p),MP2/6-311 q G(d,p),B3LYP/6-31G(d),B3LYP/6-31 G(d,p) and B3LYP/6-311 G(d,p) levels.In the H-bond N-H…O,the calcu-lated blue shift of N-H stretching frequency is in the vicinity of 120 cm~(-1) and this is indeed the largest theoreticalestimate of a blue shift in the X-H…Y H-bond ever reported in the literature.From the natural bond orbital analy-sis,the red-shifted H-bond O-H…O can be explained on the basis of the dominant role of the hyperconjugation.For the blue-shifted H-bond N-H…O,the hyperconjugation was inhibited due to the existence of significant elec-tron density redistribution effect,and the large blue shift of the N-H stretching frequency was prominently due tothe rehybridization of sp~n N-H hybrid orbital.     

Natural bond orbital population analysis of para-substituted O-nitrosyl carboxylate compounds

Theoretical study of several para-substituted O-nitrosyl carboxylate compounds has been performed using density functional B3LYP method with 6-31G(d,p) basis set. Geometries obtained from DFT calculation were used to perform natural bond orbital analysis. It is noted that weakness in the O₃–N₂ sigma bond is due to $ n_{{{\text{O}}_{1} }} \to \sigma_{{{\text{O}}_{3} - {\text{N}}_{2} }}^{*} Theoretical study of several para-substituted O-nitrosyl carboxylate compounds has been performed using density functional B3LYP method with 6-31G(d,p) basis set. Geometries obtained from DFT calculation were used to perform natural bond orbital analysis. It is noted that weakness in the O₃–N₂ sigma bond is due to n_\textO1 ? s_{\textO3 - \textN2} ^* n_{{{\text{O}}_{1} }} \to \sigma_{{{\text{O}}_{3} - {\text{N}}_{2} }}^{*} delocalization and is responsible for the longer O₃–N₂ bond lengths in para-substituted O-nitrosyl carboxylate compounds. It is also noted that decreased occupancy of the localized s_{\textO3 -\textN2} \sigma_{{{\text{O}}_{3} --{\text{N}}_{2} }} orbital in the idealized Lewis structure, or increased occupancy of s_{\textO3 - \textN2} ^* \sigma_{{{\text{O}}_{3} - {\text{N}}_{2} }}^{*} of the non-Lewis orbital, and their subsequent impact on molecular stability and geometry (bond lengths) are related with the resulting p character of the corresponding sulfur natural hybrid orbital of s_{\textO3 -\textN2} \sigma_{{{\text{O}}_{3} --{\text{N}}_{2} }} bond orbital. In addition, the charge transfer energy decreases with the increase of the Hammett constants of substituent groups and the partial charges distribution on the skeletal atoms may approve anticipating that the electrostatic repulsion or attraction between atoms can give a significant contribution to the intra- and intermolecular interaction.     

Experimental and calculated momentum densities for the valence orbitals of carbon tetrafluoride

Carbon tetraflouoride has been investigated by binary (e,2e) spectroscopy at 1200 eV impact energy. Binding energy spectra (10–60 eV) at azimuthal angles of 0° and 8° are reported and are found to be in quantitative agreement with a previous Green's function calculated spectrum. Momentum distributions corresponding to individual orbitals are also reported and compared with theoretical momentum distributions evaluated using double-zeta quality SCF wavefunctions. Excellent agreement between experimental and theories is found for the strongly bonding 3t₂ orbital and the antibonding 4a₁ orbital but agreement is less good for the outermost non-bonding orbitals. Intense structure due to molecular density (bond) oscillation is observed experimentally in the region above 1.0 a_o^?1 in the case of the non-bonding 4t₂ orbital. It is also notable that the measured 4a₁ momentum distribution exhibits an extremely well-defined “p” character with clear separation between the s and p components. Contour maps of the position-space and momentum-space orbital densities in the F-C-F plane of the molecule are used to provide a qualitative interpretation of the features observed in the momentum distribution. In order to further extend momentum-space chemical concepts to three-dimensional systems, constant density surface plots are also used to give a more comprehensive view of the density functions of the CF₈ molecule.     

Theoretical Studies on the Mechanistic Insertions of Singlet Methylene and Halomethylene into Polar S‒H Bonds of Methanethiol,Ethanethiol, 1-Propanethiol and 2-Propanethiol

Abstract

The insertion of ¹CH₂, ¹CHF, ¹CF₂,¹CHCl, and ¹CCl₂ into primary and secondary polar S?H bonds of methanethiol, ethanethiol, 1-propanethiol, and 2-propanethiol have been investigated at HF (Hartree–Fock), MP2 (Møller–Plesset Perturbation Theory), and DFT (density functional theory) levels using 6-31G (d, p) basis set. The insertions follow a two-step mechanism. The potential energy surface exploration identifies ylide-like structures undergoing the 1,2-sigmatropic hydrogen shift concertedly giving the thioether product. But ¹CF₂ forms weak complexes involving 1,2-hydrogen shift. The barrier height in the concerted mechanism varies with the type of carbene moiety and S?H bond. The initial interaction seems to be a function of HOMO (highest occupied molecular orbital) and LUMO (lowest unoccupied molecular orbital) energies of thiols and carbenes, respectively. The natural bond orbital charge analysis showing a net charge flow from the substrate thiol to the reagent carbene at the transition states corroborates this fact.     

Observation of Interference Effects in (e, 2e) Electron Momentum Spectroscopy of SF6 (cited: 1)

Two-dimensional electron density map (2D map) of binding energy and relative azimuthal angle (i.e., momentum) for the outer-valence molecular orbitals of SF₆ has been measured by a highly sensitive electron momentum spectrometer with noncoplanar symmetric geometry at the impact energy of 1.2 keV plus binding energy. The experimental electron momentum profiles for the relevant molecular orbitals have been extracted from the 2D map and interpreted on the basis of the quantitative calculations using the density functional theory with B3LYP hybrid functional. For the outermost F2p nonbonding orbitals of SF₆, the interference patterns are clearly observed in the ratios of the electron momentum profiles of molecular orbitals to that of atomic F2p orbital.     

The substitution effect on heavy versions of cyclobutadiene

The structural and electronic characteristics of the M₄R₄ with M = C, Si, Ge and R = H, F, Cl, OH, MgH, BH₂, NH₂ Li are studied by ab initio calculations based on density functional theory using the hybrid B3LYP functional and 6‐311++G* basis set. The results of natural bond orbital analysis (NBO), the analysis of structural parameters (bond lengths and bond angle, dihedral angle), atoms in molecules based theory (AIM) topological parameters such as the characteristics of bond critical points (electron densities and their Laplacians) leads to the conclusion that interamolecular interaction due with OH, MgH₂, and NH₂ substitutions are different from other derivatives. The cyclobutadiene ring and its heavy versions display very different geometrical structures. The cations and anions of C₄R₄, Si₄R₄, and Ge₄R₄ were studied to determine the effect of substitution on structure and stability. It has been shown that substitutions with ability of forming hydrogen bonds, bound to the silicon and germanium atoms are able to change the properties of the four‐member rings more than the other substitutions. Comprehensive analyses of calculated NICS (nucleus‐independent chemical shifts), polarizability, electrophilicity, and electron density are done. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

Structural and Electron Density Studies on a Chromium(IV)-Oxo Complex [CrIV(O)(TMP)]

The electron density distribution of a chromium(IV)-oxo complex, [Cr^IV(O)(TMP)] (TMP = 5,10,15,20-tetrakis-p-methoxyphenyl porphyrin), is investigated by molecular orbital calculation. The molecular and crystal structure of the compound is studied by x-ray diffraction. It belongs to the space group 1 2, Z = 2, a = 14.979(4) Å, b = 9.752(3), c = 15.605(3) Å, β = 100.97(2)°, V = 2238(1) ų, Mo Kα radiation λ = 0.7107 Å, R = 4.9%, Rw = 3.5% for 3575 observed reflections. Cr is five-coordinated in a square pyramidal fashion with the Cr atom located 0.42 Å toward the oxo-ligand. Deformation density maps are derived from the single point molecular orbital calculation on the basis of HF and DFT(density functional theory) calculations. The accumulation of deformation density along the C-H, C-C, C-N and C-O bonds in the porphyrin ligand is well represented. The asphericity in electron density around the Cr ion is clearly demonstrated. Natural bond orbital analysis (NBO) reveals that the Cr-O_oxo is actually a triple-bond character (σ²π⁴) and the four N of pyrrole serves as a σ-donor to Cr. The Cr-N_pyrrole bond is essentially a dative bond d-Orbital populations of Cr derived from both calculations are in good agreement with each other. Planar d_π-orbital is the most populated, which is in accord with the prediction from crystal field theory. Detail bond characterization of the Cr-L, multiple bond is discussed.     

Methane Chemisorption on Oxide-Supported Pt Single Atom

Methane chemisorption has been recently demonstrated on the rutile IrO₂(110) surface. However, it remains unclear how the general requirements are for methane chemisorption or complexation with a single atom on an oxide surface. By exploring methane adsorption on Pt₁ substitutionally doped on many rutile-type oxides using hybrid density functional theory, we show that the occupancy of the Pt d_z² orbital is the key to methane chemisorption. Pt single atom on the semiconducting or wide-gap oxides such as TiO₂ and GeO₂ strongly chemisorbs methane, because the empty Pt d_z² orbital is located in the gap and can effectively accept σ-electron donation from the methane C−H bond. In contrast, Pt single atom on metallic oxides such as IrO₂ and RuO₂ does not chemisorb methane, because the Pt d_z² orbital strongly mixes with the support-oxide electronic states and become more occupied, losing its ability to chemisorb methane. This study sheds further light on the impact of the interaction between a Pt single atom and the oxide support on methane adsorption.     

Theoretical studies on the reaction mechanism of palladium(0)-catalyzed addition of thiocyanates to alkynes

The reaction mechanism of the Pd(0)-catalyzed alkyne cyanothiolation reaction is investigated by MP2, CCSD(T) and the density functional method B3LYP. The overall reaction mechanism is examined. The B3LYP results are consistent with the results of CCSD(T) and MP2 methods for the isomerization, acetylene insertion and reductive elimination steps, but not for the oxidative addition step. For the oxidative addition, the bisphosphine and monophosphine pathways are competitive in B3LYP, while the bisphosphine one is preferred for CCSD(T) and MP2 methods. The electronic mechanisms for the oxidative addition of thiocyanate HS-CN to Pd(PH(3))(2) and Pd(PH(3)) and for the acetylene insertion into Pd-S and Pd-CN are discussed in terms of the electron-donation and back-donation. The chemo-selectivity that acetylene inserts into the Pd-S bond rather than into the Pd-CN bond is due to the involvement of the S p orbital. It is the doubly occupied S p unhybridized orbital that donates an electron to the alkylene pi* anti-bonding orbital, which makes insertion into Pd-S bond more favorable than into the Pd-CN bond. During the insertion into the Pd-S bond, the S sp(2) hybrid orbital and unhybridized p orbital transform into each other, while the C sp hybrid orbital shifts its direction for insertion into Pd-CN bond. By using the monosubstituted acetylenes (CN, Me and NH(2)), the influence of substituents at acetylene on the chemo- and regio-selectivities is analyzed.     

An INDO-LMO and 13C NMR spectroscopic study of the C-H bonds in tetracyclo[3.2.0.02,7.04,6]heptane (quadricyclane) and tricyclo[3.1.0.02,4]hexane

Using an INDO approximation to Von Niessen's charge density localization method, the percent s character of the C atom hybrid orbitals engaged in C-H bonds is computed for a series of open-chain and cyclic saturated and unsaturated hydrocarbons. A semi-empirical linear relationship is found between these quantities and the experimental nuclear spin-spin coupling constants J_CH (standard deviation 4·98 Hz). The experimental values of J_CH were measured for quadricyclane (1) and tricyclo[3.1.0.0^2,4]hexane (2) and were shown to be in fair agreement with the theoretical predictions. An analogous relationship is also established between the percent s character of the involved C atom hybrid orbital and the C-H bond distance, the standard deviation being 0·0040Å. This relation is used in order to predict the different C-H bond lengths in the vibrational ground state of 1 and 2, for which equal CH distances were assumed in the analysis of electron diffraction experiments. The results indicate that molecular geometries can be refined with the use of semi-empirical correlations of the above mentioned type.     

Electronic charge density and mean kinetic energy of lithium orbitals in LiH,LiH+, Li2, Li2+, LiH2+, and Li2H+

The electron density near the lithium nucleus in the species LiH, LiH⁺, Li₂, Li₂⁺, LiH₂⁺, and Li₂H⁺ was analyzed by transforming the SCF molecular orbitals into a sum of atomic contribnutions, for both core and valence orbitals. These “hybrid-atomic” orbitals were used to compare: electron densities, orbital polarizations, and orbital mean kinetic energies with the corresponding lithium atom quantities. Core-orbital electron densities at the lithium nucleus were observed to increase by up to 0.5% relative to the lithium atom 1s orbital. Lithium cores also exhibited polarization but, surprisingly, in the direction away from the internuclear region. Similar dramatic changes were seen in the electron densities of the valence orbitals of lithium: The electron density at the nucleus for these orbitals increased two-fold for homonuclear species and twenty-fold for heteronuclear triatomic species relative to the electron density at the nucleus in lithium atom. The polarization of the valence orbital electronic charge, in the vicinity of the lithium nucleus, was also away from the internuclear region. The mean “hybrid-atomic” orbital kinetic energies associated with the lithium atom in the molecules also showed changes relative to the free lithium atom. Such changes, accompanying bond formation, were relatively small for the lithium core orbitals (within 0.2% of the value for lithium atom). The orbital kinetic energies for the lithium valence electrons, however, increased considerably relative to the lithium atom: By a factor of about 2 in homonuclear diatomics, by a factor of 7 in heteronuclear diatomics, and by a factor of 11 in the triatomic species. In summary, the total electronic density (core plus valence) at the lithium nucleus remained remarkably constant for all of the species studied, regardless of the effective charge on lithium. Thus, the drastic changes noted in the individual lithium orbitals occurred in a cooperative fashion so as to preserve a constant total electron density in the vicinity of the lithium nucleus. In all cases, bond formation was accompanied by an increase in the orbital kinetic energy of the lithium valence orbital. We suggest that these two observations represent important and significant features of chemical bonding which have not previously been emphasized.     

Natural bond orbital analysis of some S‐nitrosothiols biological molecules

Theoretical study of several S‐nitrosothiols biological molecules has been performed using quantum computational ab initio RHF and density functional B3LYP and B3PW91 methods with 6‐31G(d,p) basis set. Geometries obtained from DFT calculations were used to perform natural bond orbital (NBO) analysis. It is noted that the weakness in the S? N sigma bond is due to n_O1→σ delocalization and is responsible for the longer S? N bond length in S‐nitrosothiols. It is also noted that decreased occupancy of the localized σ_SN orbital in the idealized Lewis structure or increased occupancy of σ of the non‐Lewis orbital, and their subsequent impact on molecular stability and geometry (bond lengths) are related with the resulting p character of the corresponding sulfur natural hybrid orbital of σ_SN bond orbital. In addition, the charge transfer energy decreases with the increasing of the Hammett constants of substituent groups, and the partial charge distribution on the skeletal atoms shows that the electrostatic repulsion or attraction between atoms can give a significant contribution to the intramolecular and intermolecular interaction. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

An Ab Initio calculation of the spin dipole-dipole parameters for methylene

The electron spin dipole-dipole interaction in CH₂ has been calculated as a function of bond angle with configuration-interaction wave functions built from contracted gaussianlobe basis functions. The values D = 0.781 cm^?1 and E = 0.050 cm^?1 were obtained for the spin dipole-dipole contribution to these parameters for the best CI wave function at the equilibrium geometry. The angular dependence of D shows that the assumption of perfect orbital following is not valid. Based on previous estimates of the spin-orbit contribution to D, the total D is estimated to be 0.9 ± 0.1 cm^?1 which is higher than the current experimental value 0.76 ± 0.02 cm^?1.