Ab Initio MO Method Research Articles

Graph theoretical enumeration of topology-distinct structures for hydrogen fluoride clusters (HF)n (n ≤ 6).

A graph theoretical procedure to generate all the possible topology-distinct structures for hydrogen fluoride (HF) clusters is presented in this work. The hydrogen bond matrix is defined and used to enumerate the topology-distinct structures of hydrogen fluoride (HF)n (n = 2-8) clusters. From close investigation of the structural patterns obtained, several restrictions that should be satisfied for a structure of the HF clusters to be stable are found. The corresponding digraphs of generated hydrogen bond matrices are used as the theoretical framework to obtain all the topology-distinct local minima for (HF)n (n ≤ 6), at the level of MP2/6-31G**(d, p) of ab initio MO method and B3LYP/6-31G**(d, p) of density functional theory method. For HF clusters up to tetramers, the local minimum structures that we generated are same as those in the literature. For HF pentamers and hexamers, we found some new local minima structures which had not been obtained previously.

141 Effect of ligand-binding on specific interactions between DNA and regulatory protein: molecular simulations based on MD and ab initio fragment MO methods

The transcriptional mechanism of gene information from DNA to mRNA in a cell is essentially controlled by DNA-binding regulatory proteins such as lactose repressor protein (LacR) and catabolite act...

Vibrational assignment and vibronic interaction for NO3 in the ground electronic state

Two important problems exist for the NO3 free radical. One is the frequency of the degenerate N–O stretching mode ν3. It has been assigned to a band at 1492cm−1 (Assignment I), whereas Stanton calculated it by an ab initio MO method to be around 1000cm−1 (Assignment II). The second concerns an anomalous ν4 progression, which appeared in the photoelectron spectra of the NO3 anion and was accounted for by Herzberg–Teller (H–T) mechanism, but the interaction parameter derived was too large. The present study critically examines Assignment II and the H–T vibronic interaction model against the results of high-resolution infrared (IR) spectroscopy supplemented with dispersed fluorescence (DF), and concludes Assignment I to be correct and the H–T mechanism to be complemented by a new vibronic interaction model, based upon the observations: (1) Stanton’s ab initio MO ν3 appeared in neither IR nor DF spectra, (2) only one A–E type subband was present in the Z−ν4 hot band (Z denotes the upper state of the 1492cm−1 band), at variance with the two predicted by Assignment II, (3) the ℓ-type doubling constant and the first-order Coriolis coupling constant derived for the Z state by assuming Assignment II were not acceptable, and (4) anomalous features expected from the H–T vibronic interaction model for the ν4 fundamental state were not observed at all. Infrared spectroscopic results on a few 2E′ degenerate states indicated that the first-order Coriolis coupling constant and the effective spin–orbit interaction constant were closely correlated, suggesting that the unpaired electron azimuthal motion was affected much by that of the degenerate vibrational mode. This sort of vibronic interaction has been well known for linear polyatomic free radicals in 2Σ electronic states with a bending mode singly excited. A similar vibronic interaction should be present also in symmetric-top free radicals, where a degenerate vibrational mode is singly excited. However, few examples have been reported and the NO3 radical is perhaps the first case, where the unpaired electron was shown to be strongly coupled with an excited degenerate vibrational mode, as was evidenced in the observed IR and DF spectra.

Theoretical studies of the structures and local aromaticity of conjugated polycyclic hydrocarbons using three aromatic indices

The structures and local aromaticity of some conjugated polycyclic hydrocarbons (from the butadienoid, acene, and phenylene series) are studied using ab initio MO and density functional methods. The aromaticities of the molecules are estimated using three indices: the nucleus-independent chemical shift (NICS), the harmonic oscillator model of aromaticity (HOMA), and the index of deviation from aromaticity (IDA). Assessment of the relationships between the structures and the aromatic indices shows that the IDA values correspond best to the characteristics of the conjugated polycyclic hydrocarbon structures.

An Efficient Local Molecular Dynamics Polymerization Simulation Combined with an Ab Initio MO Method.

A new local ab initio molecular dynamics method, namely elongation molecular dynamics (ELG-MD) is proposed for highly efficient simulations of aperiodic polymer systems. ELG-MD combines the elongation method (ELG) with the Gear predictor corrector (GPC) algorithm of molecular dynamics simulation. In this method, the local gradients acting on the atom’s nucleus in the active region are calculated by the ELG method while the equations of the nucleus’s motion are solved by the GPC algorithm. In this work, the first application of this ELG-MD method is described to investigate the stable conformation of polyglycine with surrounding water molecules. The water effects on the structure of polyglycine are examined. The ELG-MD simulations show that the formation of the polyglycine helix is strongly induced by the hydrogen bonds observed in two types of H-bond rings.

Ab initio MO Theory – An Important Tool in Foldamer Research: Prediction of Helices in Oligomers of ω‐Amino Acids

AbstractThe enormous developments of computer technologies allow the broad employment of ab initio MO theory in foldamer research. In this review, we demonstrate the efficiency and reliability of ab initio MO methods for the description of the helix formation in oligomers of ω‐amino acids on the basis of representative examples. Thus, ab initio MO theory successfully accompanies foldamer research by confirmation and interpretation of experimental results and stimulation of future experiments. The high predictive power of the methods opens the way to novel structure classes with special properties. Nowadays, ab initio MO theory has become an inherent part in the arsenal of methods applied in foldamer research.

19F NMR study on the complex of fluorinated vitamin D derivatives with vitamin D receptor: elucidation of the conformation of vitamin D ligands accommodated in the receptor.

Nuclear receptors mediate allosteric communications where ligand binding initiates a cascade of signal transduction. The interaction of vitamin D with vitamin D receptor (VDR) was investigated by (19)F NMR spectroscopy of the complexes of three fluorinated vitamin D derivatives with the full-length rat VDR-LBD. In the (19)F NMR spectra of the VDR-ligand complexes, the A-ring of 4,4-difluoro-1,25(OH)2D3 was revealed to adopt β-conformation in the VDR in solution, and the spectra were shown to be dependent on the dissociation constant. While the complex of 4,4-difluoro-1,25(OH)2D3 with VDR exhibited a clear distinguishable (19)F NMR spectrum, those of (19)F-1,25(OH)2D3 stereoisomers, which have 10-fold higher VDR affinity than 4,4-difluoro-1,25(OH)2D3, did not. The solid-phase NMR technique was useful for (19)F-1,25(OH)2D3 stereoisomers. The fluorinated vitamin D derivatives showed marked changes in the chemical shift (Δ4-19.7 ppm) upon VDR-complex formation, and the ab initio MO method suggested that van der Waals interactions play a major role in the complex formation.

The [2 + 2 + 2] mechanisms of trimerization of three ethynes and monosilaethylenes

The mechanisms of [2 + 2 + 2] reactions of three ethynes and monosilaethylenes to form benzene and 1,3,5-trisilacyclohexane were studied by ab initio MO methods. The reaction mechanisms were analyzed by configuration interaction/localized molecular orbital/CASSCF calculations. Although the [2 + 2 + 2] reaction of ethyne is typically “homologous” concerted, that of monosilaethylene is polarized (ionic-cyclic) one-step reaction. In addition, the aromaticity along the intrinsic reaction coordinate pathway was studied using the index of deviation from aromaticity. Although the transition state of trimerization of ethyne does not have an aromatic nature for the σ- and π-bonds formation system, the crossing point of the σ-bond formation and π-bond breaking shows an aromatic nature.

NBO analysis of polar and steric effect using the axial-equatorial equilibrium of cyclohexyl acetates as a probe

The proportion of the axial conformer increases in the ax ⇌ eq equilibrium of cyclohexyl acetates (RCOOC6H11, R=Me, Et, iPr, tBu, CH2Cl, CHCl2, CCl3, CH2Br, CHBr2, CBr3) with the increasing size of the acyloxy substitution. The nature of this unexpected steric substituent effect, which is opposite to general stereochemical concepts, was studied by means of ab initio MO method, accompanied by NBO and isodesmic calculations. NBO parameters seem to be good descriptors for quantitative prediction of the experimental ΔG° value of the title conformational equilibrium. The origin and propagation of the substituent effect of the polar substitutions (CH2Cl, CHCl2, CCl3, CH2Br, CHBr2, CBr3) differ, however, from those of the pure alkyl (Me, Et, iPr, tBu) substitutions. The ΔG° value of the polar derivatives depends on the qC8 charges, on the occupation of the σC1O7∗ orbital and on the hyperconjugative πCO∗→σC10X∗ and σC10-X→πCO∗ interactions. The substituent sensitivity of these NBO parameters for the two conformers differ to the effect that the ax ⇌ eq equilibrium is shifted to the left side with increasing electron withdrawing character of the acyloxy group. The ΔG° values of the alkyl derivatives are interpreted in terms of the calculated dipole moments. The destabilization in the non-polar medium (the experimental ΔG° values used were measured in CD2Cl2) due to the enhanced dipolar character is more prominent in the case of the equatorial alkyl conformers. As the consequence, the ax ⇌ eq equilibrium is shifted to the left despite the increasing size of the R group when going from Me to tBu substitution.

Detailed chemical kinetic mechanisms of ethyl methyl, methyl tert-butyl and ethyl tert-butyl ethers: The importance of uni-molecular elimination reactions

A reaction mechanism of ethyl methyl ether (EME), methyl tert-butyl ether (MTBE) and ethyl tert-butyl ether (ETBE) for pyrolysis and oxidation have been constructed using the same method applied to di-ethyl ether (DEE) in our recent work [1]. The mechanism, comprising of 1051 reactions involving 215 species, was tested against the experimental data obtained using shock tubes with good agreement. It was found that the uni-molecular elimination reaction has a larger influence on the pyrolysis and oxidation of MTBE and ETBE compared to EME and DEE at high temperatures. The energy barrier height between reactants and transition states of molecular elimination reactions calculated by high level ab initio MO methods has revealed the difference in reactivity among the four ethers. It is also shown that ETBE or MTBE inhibit the reactivity of an equi-molar 2% mixture of hydrogen and oxygen, whereas EME and DEE do not inhibit reactivity.

Theoretical Studies on Myers−Saito and Schmittel Cyclization Mechanisms of Hepta-1,2,4-triene-6-yne

The mechanisms of the Myers-Saito cyclization and the Schmittel cyclization of hepta-1,2,4-triene-6-yne are studied by ab initio multireference MO methods (CASSCF and MRMP2 methods). For the Myers-Saito cyclization, two transition states with C(s) and C₁ symmetries are located. The transition state with C1 symmetry is only 1.5 kcal/mol lower in energy than that with C(s) symmetry at the MRMP2 calculation level. The obtained activation energy at the transition state with C₁ symmetry and the reaction energy are 16.6 and 16.2 kcal/mol exothermic, respectively. For the Schmittel cyclization, two transition states with C(s) and C₁ symmetry are also obtained. The transition state with C₁ symmetry is 7.9 kcal/mol lower in energy than that with C(s) symmetry. The transition state with C₁ symmetry for Schmittel cyclization is 6.7 kcal/mol higher in energy than that for the Myers-Saito cyclization. The reaction mechanisms are analyzed by a CiLC-IRC method. The interactions of orbitals for the Myers-Saito and Schmittel cyclizations can be distinguished.

Theoretical studies on the cycloaddition reaction of ethylene and formaldehyde

The potential energy surface of cycloaddition (H2CCH2 + H2CO) has been investigated by using the ab initio SCF MO method at extended (3–21G) level. All the critical points were optimized by energy gradient technique and characterized by computing the Hessian matrices with analytic method. The results of computations indicate that: (i) Stepwise reactions involving diradicaloid intermediates and transition states are more favorable than the concerted ones. (ii) There are two compatible stepwise reaction mechanism, one is to form C—C bond firstly, while the other is to form C—O bond at first. (iii) For the reverse reaction-thermolysis of oxetane, the cleavage of C—O bond is preferred over that of C—C bond.

Mechanism of the CH 3NH 2–HNO 2 reaction: Ab initio DFT/TST study

The methyl amine-nitrous acid reaction in gas phase has been studied by ab initio MO and DFT methods at the B3LYP and MP2 levels using 6-31++G(d,p) basis set. Minima on the potential energy surface (PES) were characterized by absence of any imaginary frequency and the transition states by single imaginary frequencies. Intrinsic reaction coordinate method was used to find the minimum energy paths along which reactants and products are connected to the transition states. The reaction involves a number of steps: bimolecular decomposition of nitrous acid to form the ion-pair O N +… −ONO (as revealed by NPA), is the first step and is theoretically found to be the rate determining step in compliance with the experimental findings. Subsequently, a proton shuttle mechanism operates resulting finally in the formation of methanol and diazomethane as substitution and elimination product, respectively; the former is identified as the major product on the basis of computed rate constants using the transition state theory. Cleavage of old bonds and formation of new bonds during the different steps have been monitored by the study of the electronic population arrangement and the calculated IR spectra of the species occurring at the minima of the PES. A stepwise mechanism of the title reaction is thus theoretically established.

The Role of Bridging Group of Cyclopentadienyl Ligands for the Ziegler–Natta Catalysis: Theoretical Study

The potential energy surfaces of the initial reactions of ethylene insertion for the Ziegler–Natta catalysis with bridging groups of Cp ligands were studied by ab initio MO and density functional methods. Three metals (Ti, Zr, and Hf) in the Zeigler-Natta catalysis and eight bridging groups (BH, CH2, NH, O, AlH, SiH2, PH, and S) were treated. For the complex formation between ethylene and metallocenes, two type structures (vertical and horizon) were found. The vertical type structures are more stable in energy than the horizon types. The formation energy of the complex between ethylene and the metallocenes by incorporation of bridging atom or group is related to the geometrical hindrance and the bond interaction as shown in the case of boron bridging system.

Classification of OH Bonds and Infrared Spectra of the Topology-Distinct Protonated Water Clusters H3O+(H2O)n−1 (n ≤ 7)

Rooted digraphs are used to represent the features of a protonated water (PW) cluster, and we obtain all possible topology-distinct patterns corresponding to PW clusters containing up to seven water molecules. From close investigation of the structural patterns obtained, several restrictions that should be satisfied in the stable structures of PW clusters are found. The generated hydrogen bond (HB) matrices of the restrictive rooted digraph are used as the theoretical framework to obtain all of the local minima on the potential energy surfaces of those PW clusters by the use of ab initio MO and DFT methods. For PW pentamers, hexamers, and heptamers, some new local minimum structures were found that were not previously obtained. We classify all of the O-H bonds in PW clusters up to heptamer into nine types according to the difference in the hydrogen bonding pattern; each type is accompanied by a specific range of stretching frequency. The ranges of stretching frequencies of different types of O-H in PW clusters are systematically classified.

Simulation of SIMS for monomer and dimer of lignin under the assumption of thermal decomposition using QMD method

The thermal decomposition of the monomer and dimer of lignin has been simulated by a quantum molecular dynamics (DMD) method. In the calculation, we controlled the total energy of the system using Nóse-Hoover thermostats in the total energy range of 0.69–0.95 eV, and the sampling position data with a time step of 0.5 fs were carried out up to 3000 (1.5 ps) or 5000 (2.5 ps) steps in ab initio and semiempirical MO methods, respectively. We obtained the thermally decomposed fragments with positive, neutral and negative charges from SCF MO calculation at each data of the last MD step, and simulated the fragment distribution of the monomer and dimer lignins from the last step in 30–40 runs. Simulated mass numbers of positively and negatively charged fragments for lignin monomer and dimer showed considerably good accordance with the experimental results in TOF-SIMS observed by Saito and co-workers.

Heterocycle-Based Isomeric Chromophores with Substantially Varying NLO Properties: A New Structure−Property Correlation Study

A number of heterocycle-based aromatic and quinonoid molecular systems have been considered for the theoretical study of their electric response properties. The nonlinear optical (NLO) parameters have been calculated by using the ab initio MO and DFT methods. An approximate scheme for calculating the first hyperpolarizability (beta) and second hyperpolarizability (gamma) in the framework of the sum-over-state (SOS) method have been proposed by exploiting the generalized Thomas-Kuhn sum rule (TK-SR). The NLO properties in the present scheme can be evaluated solely from the ground-state dipole moment (mu) and linear polarizability (alpha) and have been found to correlate fairly with the ab initio calculated values. The approximate scheme can be reasonably used to explain the wider range of variation of higher-order polarizabilities in terms of the above quantities. The position of the N atom in the thiazole ring at the ortho position (versus meta position) to the acceptor increases beta and decreases gamma for aromatic compounds, while the reverse trend is found with quinonoid compounds. In the case of the pyridine ring, the shifting of the N atom toward the acceptor enhances gamma, with insignificant variation of beta predicted for both the aromatic and quinonoid molecules. The negative contribution of the cubic polarizability of the quinonoid species increases linearly with alpha(2)/mean transition energy (Delta E).

Theoretical Analysis of Concerted and Stepwise Mechanisms of Diels−Alder Reactions of Butadiene with Silaethylene and Disilene

The concerted and the stepwise mechanisms of the Diels-Alder reactions of butadiene with silaethylene and disilene were studied by ab initio MO methods. For the reaction of butadiene and silaethylene, an asymmetric concerted process that is almost stepwise and two stepwise processes were located. For the first step of the stepwise process, the C-Si bond formation is more favorable than the C-C bond formation. The activation energy barrier of the concerted transition state is only 0.89 kcal/mol lower than that of the first-step transition state of the C-Si bond formation for the stepwise process by the CASPT2 calculation level. For the reaction of butadiene and disilene, the activation energy barrier of the concerted-type transition state constrained with Cs symmetry is about 9 kcal/mol higher than that of the stepwise transition state by the CASSCF method. The energy barrier of the first step of the stepwise reaction disappears at the CASPT2/6-311++G(d,p) calculation level including the nondynamical correlation energy, although the reaction of the butadiene with disilene occurs through the stepwise-like process.

Enumeration of Topology-Distinct Structures and Possible Stable Structures of Protonated Water Clusters, H3O+(H2O)n−1 (n≤5)

Abstract A rooted digraph is regarded as a protonated water (PW) cluster, and a hydrogen bond (H-B) matrix can represent a rooted digraph. All possible topology-distinct patterns corresponding to PW clusters containing up to 8 water molecules were enumerated by using H-B matrices. From close investigation of the structural patterns obtained, we found several restrictions that should be satisfied for a structure of the PW clusters to be stable. The generated H-B matrices of the restrictive rooted digraph were used as the theoretical framework to obtain all the topology-distinct local minima of H3O+(H2O)n−1 (n≤5), at the level of MP2/6-31G∗∗ of ab initio MO method. For PW clusters up to tetramers, the local minimum structures that we generated are same as those in the literatures. For PW pentamers, we found some new local minimum structures, which had not been obtained previously.

Ab initiostudy onN,N′,N″‐triaminoguanidine

AbstractElectronic structure calculations and second‐order delocalizations inN,N′,N′′‐triaminoguanidine (TAG) have been studied by employingab initioMO and density functional methods. There are total 10 rotational isomers on the potential energy (PE) surface ofTAG. The effect of three amino groups substitution on guanidine (Gu) has been studied in terms of the primary and the secondary electron delocalizations inTAGby employing Natural Population Analysis (NPA). An increased electron delocalization is observed in protonated triaminoguanidine (TAGP) due to the three strong intramolecular hydrogen bonds and hence accounts for its extra stability. The increase in the electron delocalization upon protonation inTAGcan be compared to that in guanidine. The absolute proton affinity (APA) ofTAGis less than that ofGu. HOMA and NICS studies have been carried out to understand electron delocalization inTAGP. Copyright © 2007 John Wiley & Sons, Ltd.