A detailed analysis of pseudorotation in PH4F

Summary Pentacoordinated molecules are thought to undergo intramolecular isomerization by the widely accepted Berry pseudorotation mechanism. Through our investigations, we have found that the actual pseudorotation for the PH₄F system is more complex than that envisioned by Berry. The potential energy surface of PH₄F is mapped out at the RHF/6-311G(d, p) level. According to the Berry mechanism, this system is expected to have two minima and two maxima; however, the system actually has two transition states and one global minimum. The minimum energy path from the highest transition state is followed to the second transition state, which in turn has a minimum energy path leading to the global minimum. Along the path between the two transition states there is a branching region. This portion of the potential energy surface is probed extensively.Dedicated to Prof. Klaus Ruedenberg     

Calculation of excited-state properties of some small molecules: Comparative study of the CNDO/S and CNDO/2-vn−1 potential methods

The transition energy and geometry of the lowest excited (nπ*) singlet and triplet states of CO, CS, HNO, H₂CO, HFCO, and F₂CO molecules are calculated by CNDO /S and CNDO /2-V_N?1 potential methods, and the results are compared with those of experimental and ab initio theoretical studies, wherever available. In the calculation of the vertical transition energy, the performance of the CNDO /S method is seen to be generally more satisfactory than that of the CNDO /2-V_N?1 potential method, while the reverse is true for the excited-state geometry. The CNDO /S method as such fails to describe the geometry of the excited state, but a combined version (CNDO /S-2) of CNDO /S and CNDO /2, as well as the CNDO /2-V_N?1 potential method is fairly successful in this regard.     

Molecular orbital theory of the hydrogen bond. XXX. Water-cytosine complexes

Ab initio SCF and SCF -CI calculations with the STO -3G basis set have been performed to investigate the structures and energies of water–cytosine complexes and the intermolecular water–cytosine surface in the cytosine molecular plane. Although there are six nominal hydrogen-bonding sites in this plane, only three dimers are distinguishable in the ground state. The most stable has an energy of ?10.7 kcal/mol, and is found in the N₁? H and O₂ region. An asymmetric cyclic structure in which the water molecule bridges adjacent N₁? H and O₂ sites is the preferred form of this dimer. The dimer in the region between O₂ and N₄? H′ of the amino group is slightly less stable at ?10.4 kcal/mol, and also has an asymmetric cyclic structure as the preferred structure, with the water molecule bridging amino N₄? H′ and N₃ hydrogen-bonding sites. The third dimer has the amino group as the proton donor to water through the hydrogen cis to C₅, and a stabilization energy of ?7.0 kcal/mol. The water-cytosine surface is characterized by deeper minima and higher barriers than the water-thymine surface and by a decreased mobility of the water molecule between adjacent hydrogen-bonding sites. Absorption of energy by the C₂?O group leads to the first n → π* excited state in which interactions of water with O₂ are broken. The water-cytosine dimers remain bound in this state, but may change structurally. In the second n → π* state interactions between water and N₃ are no longer stabilizing. As a result, the dimer in the O₂ and N₄? H′ region collapses to either a dimer with water the proton donor to O₂, or one with N₄? H′ the proton donor to water. The other two dimers remain bound. All excited dimers are destabilized on vertical excitation relative to the ground state.     

Contributions of Various Noncovalent Bonds to the Interaction between an Amide and S‐Containing Molecules

N‐Methylacetamide, a model of the peptide unit in proteins, is allowed to interact with CH₃SH, CH₃SCH₃, and CH₃SSCH₃ as models of S‐containing amino acid residues. All of the minima are located on the ab initio potential energy surface of each heterodimer. Analysis of the forces holding each complex together identifies a variety of different attractive forces, including SH???O, NH???S, CH???O, CH???S, SH???π, and CH???π H‐bonds. Other contributing noncovalent bonds involve charge transfer into σ* and π* antibonds. Whereas some of the H‐bonds are strong enough that they represent the sole attractive force in several dimers, albeit not usually in the global minimum, charge‐transfer‐type noncovalent bonds play only a supporting role. The majority of dimers are bound by a collection of several of these attractive interactions. The SH???O and NH???S H‐bonds are of comparable strength, followed by CH???O and CH???S.     

Molecular orbital studies of hydrogen bonds. IV. Hydrogen bonds in excited states of H2CO with H2O

Ab initio calculations for the interacting system of lower excited states of planar and bent H₂CO with H₂O have been carried out with a minimum basis set, using the recently proposed electron-hole potential method. The blue shifts of the η-π* transition are evaluated as 1100 and 1420 cm^?1 for the singlet and triplet transitions, respectively. In the η-π* states of bent H₂CO, the most stable geometry is one in which an H₂O hydrogen atom is coordinated to the carbon atom.     

Some remarks on the semiempirical one-center electron repulsion integrals

The identification of the stage of ionization for various kinds of one-center electron repulsion integrals, occurring when nonbonding or lone-pair electrons are considered explicitly as well as π-electrons, is discussed for conjugated organic molecules containing heteroatoms N. It is concluded that the value for the negative ions should be used for (π_Cπ_C | π_Cπ_C) in all the states but for (π_Nπ_N | π_Nπ_N) only in the π-π states. In the n-π states, the appropriate value of (π_Nπ_N | π_Nπ_N) is that of the neutral atom if the molecule contains only one N atom. If more than one N atom is involved in the molecule, some weighted mean of the values for the negative ion and for the neutral atom should be used. The value for the neutral atom is most adequate for one-center repulsion integrals other than the (ππ | ππ) type in both the π-π and the n-π states. The method of determining these integrals is also discussed. It is concluded that they are to be determined from the consideration of appropriate electron-transfer reactions except for exchange integrals. The exchange integrals are shown to have to be determined from the Slater–Condon parameters derived from the analysis of the experimental atomic energy levels. Illustrative calculations are given for the lower singlet levels of the formaldehyde, pyrazine, pyridine, and the p-benzoquinone molecule. It is found that the calculated energies of the n-π transitions become much too low unless the (ππ | ππ) values of the heteroatoms in the molecule are chosen differently in the n-π states and in the π-π states as pointed out theoretically in this article.     

Nontotally symmetric trifurcation of an SN2 reaction pathway

A new type of reaction pathway which involves a nontotally symmetric trifurcation was found and investigated for a typical S_N2‐type reaction, NC^‐ + CH₃X → NC? CH₃ + X^‐ (X = F, Cl). A nontotally symmetric valley‐ridge inflection (VRI) point was located along the C_3v reaction path. For X = F, the minimum energy path (MEP) starting from the transition state (TS) leads to a second‐order saddle point with C_3v symmetry, which connects three product minima of C_s symmetry. For X = Cl, four product minima have been observed, of which three belong to C_s symmetry and one to C_3v symmetry. The branching path from the VRI point to the lower symmetry minima was determined by a linear interpolation technique. The branching mechanism is discussed based on the reaction path curvature and net atomic charges, and the possibility of a nonotally symmetric n‐furcation is discussed. © 2015 Wiley Periodicals, Inc.     

Understanding the differences in photochemical properties of substituted aminopyrimidines

The luminescent patterns of several members of the aminopyrimidine family are very different, showing not fluorescence at all, only a fluorescence band, normal or anomalous, or dual fluorescence, depending on the substituents and on the environment (gas phase vs. polar solvents). In this work, we study the lowest excited states of several members of this family that exhibit different fluorescence patterns to try to explain their photochemistry and to understand the effect of the substituents and the environment. We have found that several excited states (local excited (LE), charge transfer (CT) and n _N?C??* states) have minima on the lowest excited potential energy surface (S₁), being their relative energy the determinant factor of the luminescent behavior. If the more stable S₁ minima are of n _N?C??* character, a non-radiative deexcitation channel is the most efficient and the system shows no fluorescence. If the CT and/or LE states are the most stable, the non-radiative deactivation channel is not accessible and the system fluoresces. The relative energies of the CT and LE minima (affected by substituents and by the presence of a polar solvent) and the different magnitude of the oscillator strength for the radiative transition to the ground state determine which emission is more efficient, giving place to normal, anomalous or dual fluorescence. The study has been carried out by CASSCF/CASPT2 computations, including the solvent effect by means of the PCM model.     

Molecular orbital theory of the hydrogen bond. 25. Water–uracil complexes in excited n → π states

Hydrogen bonding of uracil with water in excited n → π* states has been investigated by means of ab initio SCF -CI calculations on uracil and water–uracil complexes. Two low-energy excited states arise from n → π* transitions in uracil. The first is due to excitation of the C₄? O group, while the second is associated with excitation of the C₂? O group. In the first n → π* state, hydrogen bonds at O₄ are broken, so that the open water–uracil dimer at O₄ dissociates. The “wobble” dimer, in which a water molecule is essentially free to move between its position in an open structure at N₃? H and a cyclic structure at N₃? H and O₄ in the ground state, collapses to a different “wobble” dimer at N₃? H and O₂ in the excited state. The third dimer, a “wobble” dimer at N₁? H and O₂, remains intact, but is destabilized relative to the ground state. Although hydrogen bonds at O₂ are broken in the second n → π* state, the three water–uracil dimers remain bound. The “wobble” dimer at N₁? H and O₂ changes to an excited open dimer at N₁? H. The “wobble” dimer at N₃? H and O₄ remains intact, and the open dimer at O₄ is further stabilized upon excitation. Dimer blue shifts of n → π* bands are nearly additive in 2:1 and 3:1 water:uracil structures. The fates of the three 2:1 water:uracil trimers and the 3:1 water:uracil tetramer in the first and second n → π* states are determined by the fates of the corresponding excited dimers in these states.     

Interplay of noncovalent interactions in antiseptic quaternary ammonium surfactant Miramistin

The molecular and crystal structure of the widely used antiseptic benzyldimethyl{3‐[(1‐oxotetradecyl)amino]propyl}ammonium chloride monohydrate (Miramistin, MR ), C₂₆H₄₇N₂O⁺·Cl^?·H₂O, was determined by a single‐crystal X‐ray diffraction study and analyzed in the framework of the QTAIM (quantum theory of atoms in molecules) approach using both periodic and molecular DFT (density functional theory) calculations. The various noncovalent intermolecular interactions of different strengths were found to be realized in the hydrophilic parts of the crystal packing (i.e. O—H…Cl, N—H…Cl, C—H…Cl, C—H…O and C—H…π). The hydrophobic parts are built up exclusively by van der Waals H…H contacts. Quantification of the interaction energies using calculated electron‐density distribution revealed that the total energy of the contacts within the hydrophilic and hydrophobic regions are comparable in value. The organic MR cation adopts the bent conformation with the head group tilted back to the long‐chain alkyl tail in both the crystalline and the isolated state due to stabilization of this geometry by several intramolecular C—H…π, C—H…N and H…H interactions. This conformation preference is hypothesized to play an important role in the interaction of MR with biomembranes.     

Synthesis and supramolecular features of hybrid POM/onium solid-state assemblies

Abstract

Polyoxomolybdate-based organic?inorganic hybrid architectures were synthesised and characterised by X-ray crystallography. The supramolecular assemblies present rows of metallic clusters H-bonded by ammonium cations, with a 1:2 molybdate/ammonium ratio. The organic moieties of the ammonium cations establish hydrophobic contact among them such as van der Waals, C–H?π and π?π interactions that stabilise the supramolecular architectures. In particular, for compound 5 the n-alkyl tails pack closely together giving a lipid-like bilayer. In compound 6, the aromatic phenyl rings of the organic cation allow the stabilisation of the supramolecular architecture by C–H?π and π?π interactions. Regarding the X-ray structure of the compound 11, the tetraanionic octa-molybdate [Mo₈O₂₆]^4? cluster is surrounded by four ethyl-triphenyl-phosphonium cations. Running along the b-axis open channels are occupied by DMF solvent molecules. Interestingly, a soaking experiment in n-pentane with the corresponding crystals of compound 11 afforded to a crystal structure very different from the native one.     

Quantenchemische untersuchungen zum mechanismus der elektrophilen substitution. I. Zur potentialhyperfläche des systems benzol/h+

Results of semiempirical calculations (CNDO/2-FK and MINDO/2 methods) for the σ-π complex problem on protonated benzene are given and compared with previous ones. The semiempirical methods were chosen according to the agreement of their results with new theoretical energy data (E_HF + E_korrel) concerning the classical–nonclassical problem of protonated ethylene. By these methods the corresponding part of the energy surface of the benzene/H⁺ system is simulated. The stationary points of this surface are found by a gradient method with complete optimization of the geometry. On the basis of this method we determined the energy profile of a reaction coordinate between the classical (σ-complex) and nonclassical (π-complex) cation. The so called strong π-complex is a saddle point between two σ-complex minima and can be interpreted as transition state of 1,2-proton shifts. Hypotheses for possible minimum energy paths of electrophilic attacks in the given region of the surface are discussed.     

On the existence of SH3, SeH3, and TeH3: Discrepancies between all-electron and pseudopotential calculations

Ab initio calculations using both pseudopotential and double and triple-ζ all-electron basis sets, with and without electron correlation (MP2, QCISD), have been performed on the λ⁴-sulfanyl (SH₃), λ⁴-selanyl (SeH₃), and λ⁴-tellanyl (TeH₃) radicals. All-electron basis sets of double-ζ quality predict that SH₃ and SeH₃ correspond to transition states on their respective potential energy surfaces. In contrast, the pseudopotentials of Hay and Wadt predict that SH₃ and SeH₃ correspond to local minima at the QCISD level of theory while the pseudopotentials of Christiansen and Stevens predict transition states. By comparison, TeH₃ proved to be a local minimum at all levels of theory. Interestingly, when a very large (triple-ζ) all-electron basis set was used, SH₃ proved to be a transition state; however, in this instance the potential energy surface was found to be much flatter than in the case for which a double-ζ basis set was used, suggesting that further improvements in the basis set may lead to a local minimum. Further improvements in the all-electron selenium basis also led to a local minimum for SeH₃ at the QCISD level of theory. © 1995 by John Wiley & Sons, Inc.     

Isomerization study of C5H5NO molecules

The complex potential energy surface (PES) for the isomerization of C₅H₅NO species, including 18 isomers and 23 interconversion transition states, is probed theoretically at the B3LYP/6‐311++G(d,p) and MP2//B3LYP/6‐311++G(d,p) levels of theory. The geometries and relative energies for various stationary points were determined. The zero‐point vibrational energy (ZPVE) corrections have been made to calculate the reliable energy. We predicted a six‐membered ring structure as a global minima isomer I, which is 118.49 and 131.48 kcal · mol^?1 more stable than the least stable, four‐ and three‐membered ring isomer VIII at B3LYP and MP2//B3LYP levels of theory, respectively. The isomers and interconversion transition states have verified by frequency calculation. The intrinsic reaction coordinates (IRC) calculations have been performed to confirm that each transition state is linked by the desired reactants and products. The isomer stability has been studied using relative energies, chemical hardness, and chemical potential. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

A family of enneanuclear iron(II) single-molecule magnets

Complexes [Fe₉(X)₂(O₂CMe)₈{(2‐py)₂CO₂}₄] (X^?=OH^? ( 1 ), N₃^? ( 2 ), and NCO^? ( 3 )) have been prepared by a route previously employed for the synthesis of analogous Co₉ and Ni₉ complexes, involving hydroxide substitution by pseudohalides (N₃^?, NCO^?). As indicated by DC magnetic susceptibility measurements, this substitution induced higher ferromagnetic couplings in complexes 2 and 3 , leading to higher ground spin states compared to that of 1 . Variable‐field experiments have shown that the ground state is not well isolated from excited states, as a result of which it cannot be unambiguously determined. AC susceptometry has revealed out‐of‐phase signals, which suggests that these complexes exhibit a slow relaxation of magnetization that follows Arrhenius behavior, as observed in single‐molecule magnets, with energy barriers of 41 K for 2 (τ₀=3.4×10^?12 s) and 44 K for 3 (τ₀=2.0×10^?11 s). Slow magnetic relaxation has also been observed by zero‐field ⁵⁷Fe Mössbauer spectroscopy. Characteristic integer‐spin electron paramagnetic resonance (EPR) signals have been observed at X‐band for 1 , whereas 2 and 3 were found to be EPR‐silent at this frequency. ¹H NMR spectrometry in CD₃CN has shown that complexes 1 – 3 are stable in solution.     

A new end-on (μ1,1) azido bridged [Zn2(L)2(Na)N3]n 1D chain derived from a trinuclear zinc complex: syntheses,crystal structures,photoluminescence properties and DFT study

A bicompartmental N₂O₄ donor symmetric Schiff base ligand has been deployed to synthesize a trinuclear zinc complex [Zn₃(L)₂Cl₂], which upon treatment with sodium azide produces a new μ_1,1-azido-bridged 1-D polymer [Zn₂(L)₂(Na)N₃]_n. Both complexes have been characterized using IR, NMR, UV–vis, and X-ray diffraction techniques. In order to have better understanding of electronic transitions of the complexes, a time-dependent DFT study has been performed. Lifetime measurements have also been performed to learn about the stability of excited states of both complexes. The average fluorescence decay lifetime has been found to be 1.42 and 0.59 ns for 1 and 2, respectively. In Hirshfeld surface mapping, X?H/H?X (X = O, Cl) contacts are found to be only 2.7% of the total surface, which indicates that no significant X?H/H?X contacts are present in either of the complexes. Unconventional interactions such as C–H?π and π?π stacking interactions are found in supramolecular architectures of both complexes.     

Excited-state intramolecular proton transfer driven by conical intersection in hydroxychromones

Nonradiative decay pathways associated with vibronically coupled S₁(ππ*)–S₂(nπ*) potential energy surfaces of 3- and 5-hydroxychromones are investigated by employing the linear vibronic coupling approach. The presence of a conical intersection close to the Franck–Condon point is identified based on the critical examination of computed energetics and structural parameters of stationary points. We show that very minimal displacements of relevant atoms of intramolecular proton transfer geometry are adequate to drive the molecule toward the conical intersection nuclear configuration. The evolving wavepacket on S₁(ππ*) bifurcates at the conical intersection: a part of the wavepacket moves to S₂(nπ*) within a few femtoseconds while the other decays to S₁ minimum. Our findings indicate the possibility of forming the proton transfer tautomer product via S₂(nπ*), competing with the traditional pathway occurring on S₁(ππ*).     

Physicochemical Characterization of Four Gadolinium(III) DTPA‐like Complexes

The analysis of ¹⁷O NMR transverse relaxation rates and EPR transverse electronic relaxation rates for aqueous solutions of the four DTPA‐like (DTPA = diethylenetriamine‐N,N,N′,N″,N″‐pentaacetic acid) complexes, [Gd(DTPA‐PY)(H₂O)]^? (DTPA‐PY = N′‐(2‐pyridylmethyl)), [Gd(DTPA‐HP)(H₂O)₂]^? (DTPA‐HP = N′‐(2‐hydroxypropyl)), [Gd(DTPA‐H1P)(H₂O)₂]^? (DTPA‐H1P = N′‐(2‐hydroxy‐1‐phenylethyl)) and [Gd(DTPA‐H2P)(H₂O)₂] (DTPA‐H2P = N′‐(2‐hydroxy‐2‐phenylethyl)), at various temperatures allows us to understand the water exchange dynamics of these four complexes. The water‐exchange lifetime (τM) parameters for [Gd(DTPA‐PY)(H₂O)]^?, [Gd(DTPA‐HP)(H₂O)₂]^?, [Gd(DTPA‐H1P)(H₂O)₂]^? and [Gd(DTPA‐H2P)(H₂O)₂] are of 585, 98, 163, and 69 ns, respectively. Compared with [Gd(DTPA)(H₂O)]^2? (τM = 303 ns), the τM value of [Gd(DTPA‐PY)(H₂O)]^? is slightly higher, but the other three complexes values are significantly lower than those of [Gd(DTPA)(H₂O)]^2?. This difference is explained by the fact that the gadolinium(III) complexes of DTPA‐HP, DTPA‐H1P, and DTPA‐H2P have two inner‐sphere waters. The ²H longitudinal relaxation rates of the labeled diamagnetic lanthanum complex allow the calculation of its rotational correlation time (τR). The τR values calculated for DTPA‐PY, DTPA‐HP, DTPA‐H1P, and DTPA‐H2P are of 127, 110, 142 and 147 ps, respectively. These four values are higher than the value of [La(DTPA)]^2? (τR = 103 ps), because the rotational correlation time is related to the magnitude of its molecular weight.     

Channels to Singlet and Triplet Phenylcarbenes in Phenyldiazomethane: A CASSCF and MRCI Study

Diazo compounds such as phenyldiazomethane (C₆H₅C(H)N₂) exhibit intriguing phenomena including the ultrafast formation of singlet carbene and the excited‐state rearrangement reaction (RIES). In this work, we have used multi‐reference configuration interaction with single and double excitations (MRCI‐SD) and complete active space self‐consistent field (CASSCF) methods to study the photodissociation dynamics of C₆H₅C(H)N₂. The equilibrium structures, transition states in the lowest three electronic states (S₁, T₁, and S₀), and S₁/S₀ and T₁/S₀ minimum‐energy crossing points both in the Franck–Condon region and on the pathway of the CN bond dissociation have been optimized. On the basis of the calculated S₁, T₁, and S₀ potential energy surfaces, we have uncovered the most efficient pathways to the lowest singlet and triplet phenylcarbenes (C₆H₅CH) in irradiated C₆H₅C(H)N₂.