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PubMed2006

Monosilicon-substituted cyanoacetylene: a computational study.

A detailed theoretical investigation of the [H,Si,C(2),N] potential energy surfaces including 28 minimum isomers and 65 interconversion transition states is reported at the Gaussian-3//B3LYP/6-31G(d) level. Generally, the triplet species lie energetically higher than the singlet ones. The former three low-lying isomers are linear HCCNSi 1 (0.00 kcal/mol), branched SiC(H)CN 12 (7.09 kcal/mol), and bent HNCCSi 7 (14.22 kcal/mol), which are separated by rather high barriers from each other and are kinetically very stable with the least conversion barriers of 32.6-70.5 kcal/mol. Two energetically high-lying isomers HCNCSi 3 (42.99 kcal/mol) and SiC(H)NC 13 (36.05 kcal/mol) are also kinetically stable with a barrier of 49.19 and 21.42 kcal/mol, respectively. Additionally, five high-lying isomers, that is, three chainlike isomers, HCCSiN 2 (55.17), HCSiNC 6 (47.80), HSiNCC 11 (78.83), and one three-membered ring isomer HN-cSiCC 19 (51.21), and one four-membered ring isomer cSiCN(H)C 27 (50.6 kcal/mol), are predicted to each have lower conversion barriers of 12-18 kcal/mol and can be considered as meta-stable species. All of the predicted 10 isomers could exist as stable or meta-stable intermediates under suitable conditions. Finally, the structural and bonding analysis indicate that the [H,Si,C(2),N] molecule contains various properties that are of chemical interest (e.g., silylene, SiC triple bonding, and conjugate SiN triple bonding and CC triple bonding, charge-transfer specie, planar aromatic specie, cumulate double bonding). This is the first detailed theoretical study on the potential energy surfaces of the series of hydrogenated Si,C,C,N-containing molecules. The knowledge of the present monohydrogenated SiC(2)N isomerism could provide useful information for more highly hydrogenated or larger Si,C(2),N-containing species.

Acetylene↗
PubMed2006

Self-modeling structure of evoked postsynaptic potentials.

With the simplicity of the synaptic structure and physiology at neuromuscular junctions (NMJs) of crayfish and the given transmitter being released in quantal packets, a detailed assessment in the fundamental processes of chemical synaptic transmission is possible. Since the quantal event is the basic element of transmission, we consider an approach to further understand the characteristics of quantal responses. In this study, we introduce a method for combining information across excitatory postsynaptic potentials (EPSPs) that are quantal in nature. The method is called self-modeling regression, known in the statistics literature as SEMOR. This method illustrates that the differing timing and heights of EPSPs can be described with four coefficients measuring affine (shift and scale) transformations of the x and y axes. We demonstrate that this relationship allows us to provide a unified schema for the many functionals currently used in the literature, such as peak amplitude, tau, latency, area under the curve, or decay time. Computer code in R is available on the internet to perform the analysis.

Animals↗
PubMed1994

Influence of slight sequence changes on the free energy of a single stranded ribonucleic acid molecule.

Single-stranded ribonucleic acid molecules take a variety of secondary structures. The free energy (g) of a given secondary structure of a molecule is calculated from the Boltzmann weighted summation over the states of this molecule taking this secondary structure. Likewise, the free energy (G) of a molecule is calculated from the summation over the states of this molecule, which takes various secondary structures. The g-value can be evaluated by Salser's method (1977, Cold Spring Harbor Symp. Quantum Biol. 42, 985-1002). By use of these values, the G-value can also be obtained. Computer studies utilizing this method reveal that there is a particular class of molecules whose G-values tend to increase when the sequences are slightly changed. As far as we examined, such molecules take few secondary structures that fulfill the following two conditions simultaneously: (i) The g-value is close to that of the optimal secondary structure. (ii) The structure is very different from the optimal secondary structure. Here, the optimal secondary structure means the one with the lowest g-value among all the secondary structures taken by the molecule.

Base Sequence↗
PubMed1990

Theoretical calculations on calcium channel drugs: is electron transfer involved mechanistically?

Theoretical studies were done on calcium channel drugs in order to gain insight into the mode of action. Empirical force field calculations with nifedipine, a calcium channel antagonist, indicate that the E-conformation at the ring juncture is lower in energy than the Z-conformation. This energy difference is only 0.2 kcal/mol when the esters in the 3- and 5-positions of the dihydropyridine (DHP) ring are both synperiplanar (sp, sp). Molecular orbital calculations on the ground and excited states in the Z-conformation with the esters in the (ap, sp) conformation show a low lying excited state with substantial intramolecular electron transfer (ET) character. This excited state is only 1.8 eV higher in energy than the ground state and corresponds to a transfer of approximately 0.3 electron from the DHP ring to the nitrobenzene moiety. We suggest that ET may play an important role in the mechanism of action, either intramolecular or, as previously proposed, intermolecular, along with lipophilicity and steric effects.

Calcium Channel Blockers↗
PubMed2006

UV-induced generation of rare tautomers of allopurinol and 9-methylhypoxanthine -- a matrix isolation FTIR study.

Monomers of allopurinol and 9-methylhypoxanthine were studied using the matrix isolation technique combined with Fourier transform infrared spectroscopy. The oxo tautomeric forms of both compounds were found to dominate in freshly deposited low-temperature argon matrices. For 9-methylhypoxanthine, a small amount of the hydroxy tautomer was also detected in an Ar matrix before any irradiation. Upon exposure of the matrices to the UV (lambda>230 nm or lambda>270 nm) light, a proton transfer photoreaction converting the oxo forms of both compounds into the corresponding hydroxy tautomers occurred. Generation of conjugated ketenes as minor photoproducts was also observed. For 4(3H)-pyrimidinone (a model compound for both allopurinol and 9-methylhypoxanthine), photoreversibility of the UV-induced oxo --> hydroxy transformation was experimentally proven by direct observation of the back hydroxy --> oxo photoreaction. The substrates (oxo tautomers) and products (hydroxy tautomers) of the observed phototransformations were identified by comparison of their IR spectra with the spectra theoretically predicted at the DFT(B3LYP)/6-31++G(d,p) level. The IR bands in the experimental spectra were assigned to the calculated normal modes.

Allopurinol↗
PubMed2003

Mathematical formulation of Leibnizian world: a theory of individual-whole or interior-exterior reflective systems.

A world model, suggested by Leibniz's monadology, is formulated as a mathematical axiomatic system. The purpose of this world model is to provide a general scheme for describing a system of individuals having consciousness or internal worlds that communicate with each other and make a unified whole world, and moreover, the latter is reflected into the respective internal worlds and appears as an external world. Examples of such monadological structure of interior-exterior (or individual-whole) reflection can be observed in bio- or socio-systems and recently in computer networks. Moreover, a most elemental version of this structure can be found in the basic level of quantum physics. The model not only gives a prototype of monadological systems but also has an evolutionary ability to produce a hierarchy of monadological systems, which are interpreted as corresponding to various levels of consciousness.

Mathematics↗
PubMed2006

Cobalt-mediated cyclic and linear 2:1 cooligomerization of alkynes with alkenes: a DFT study.

The mechanism of the cobalt-mediated [2 + 2 + 2] cycloaddition of two alkynes to one alkene to give CpCo-complexed 1,3-cyclohexadienes (cyclic oligomerization) has been studied by means of DFT computations. In contrast to the mechanism of alkyne cyclotrimerization, in which final alkyne inclusion into the common cobaltacyclopentadiene features a direct "collapse" pathway to the complexed arene, alkene incorporation proceeds via insertion into a Co-C sigma-bond rather than inter- or intramolecular [4 + 2] cycloaddition. The resulting seven-membered metallacycle 7 is a key intermediate which leads to either CpCo-complexed cyclohexadiene 5 or hexatriene 13. The latter transformation, particularly favorable for ethene, accounts, in part, for the linear oligomerization observed occasionally in these reactions. With aromatic double bonds, a C-H activation mechanism by the cobaltacyclopentadiene seems more advantageous in hexatriene product formation. Detailed investigations of high- and low-spin potential energy surfaces are presented. The reactivity of triplet cobalt species was found kinetically disfavored over that of their singlet counterparts. Moreover, it could not account for the formation of CpCo-complexed hexatrienes. However, triplet cobalt complexes cannot be ruled out since all unsaturated species appearing in this study were found to exhibit triplet ground states. Consequently, a reaction pathway that involves a mixing of both spin-state energy surfaces is also described (two-state reactivity). Support for such a pathway comes from the location of several low-lying minimum-energy crossing points (MECPs) of the two surfaces.

Alkenes↗
PubMed1996

Molecular electronic properties of a series of 4-quinolinecarbinolamines define antimalarial activity profile.

A detailed computational study on a series of 4-quinolinecarbinolamine antimalarials was performed using the semiempirical Austin model 1 (AM1) quantum chemical method to correlate the electronic features with antimalarial activity and to illuminate more completely the fundamental molecular level forces that affect the function and utility of the compounds. Ab initio (3-21G level) calculations were performed on mefloquine, the lead compound in this series, to check the reliability of the AM1 method. Electron density in specific regions of the molecules appears to play the pivotal role toward activity. A large laterally extended negative potential in the frontal portion of the nitrogen atom of the quinoline ring and the absence of negative potential over the molecular plane are crucial for the potent antimalarials. These electrostatic features are likely to be the modulator of hydrophobicity or lipophilicity of the compounds and, hence, determine their activities. The magnitude of the positive potential located by the hydroxyl hydrogen atom also correlates with potent antimalarial activity. Two negative potential regions occur near the hydroxyl oxygen and piperidyl nitrogen atoms. The two negative potential regions and the positive potential located by the hydroxyl hydrogen atom are consistent with intermolecular hydrogen bonding with the cellular effectors. The present modeling study should aid in efficient designing of this class of antimalarial agents.

Animals↗
PubMed2005

Effect of substituents on the strength of A-Cl- (A = Si, Ge, and Sn) bonds in hypervalent systems: ACl5-, ACl4F-, and A(CH3)3Cl2-.

The gas-phase strengths of the A-Cl(-) bonds in ACl(5)(-), ACl(4)F(-), and A(CH(3))(3)Cl(2)(-) (A = Si, Ge, and Sn) have been determined by measuring thresholds for collision-induced dissociation in a flowing afterglow-tandem mass spectrometer. Bond dissociation energies increase in the order Si < Ge < Sn. Replacement of the three equatorial chlorides with methyl groups weakens the bonds, while replacing one axial chloride with a fluoride strengthens the bonds. Computational results using the B3LYP model with several basis sets parallel the experimental periodic trends, but provide bond dissociation energies lower than experiment by 7-44 kJ mol(-1). MP2 computational results are in better agreement with experiment. The results are consistent with steric hindrance and electrostatic effects playing significant roles in the bonding energetics.

Computer Simulation↗
PubMed2005

Hydroxyl radical and hydroxide ion in liquid water: a comparative electron density functional theory study.

Ab initio density functional theory molecular dynamics simulations of the solvated states of the hydroxyl radical and hydroxide ion are performed using the Becke-Lee-Yang-Parr (BLYP) exchange-correlation functional (Becke, A. D. Phys. Rev. A 1988, 38, 3098. Lee, C.; Yang, W.; Parr, R. G. Phys. Rev. B 1988, 37, 785). The structures of the solvation shells of the two species are examined. It is found that the OH radical forms a relatively well-defined solvation complex with four neighboring water molecules. Three of these molecules are hydrogen bonded to the OH, while the fourth is hemibonded via a three-electron two-centered bond between the oxygen atoms of the OH and water. The activity and the diffusion mechanism of the OH radical in water is discussed in comparison with the OH- ion. Although the results are partially influenced by the tendency of the BLYP density functional to overestimate hemibonded structure, the present simulations suggest that the widely accepted picture of rapid diffusion of OH radical in water through hydrogen exchange reaction may need to be reconsidered.

Algorithms↗
PubMed2005

Spectroscopic and computational studies of aqueous ethylene glycol solution surfaces.

The combination of Monte Carlo, ab initio, and DFT computational studies of ethylene glycol (EG) and EG-water hydrogen-bonding complexes indicate that experimental vibrational spectra of EG and EG-water solution surfaces have contributions from numerous conformations of both EG and EG-water. The computed spectra, derived from harmonic vibrational frequency calculations and a theoretical Boltzmann distribution, show similarity to the experimental surface vibrational spectra of EG taken by broad-bandwidth sum frequency generation (SFG) spectroscopy. This similarity suggests that, at the EG and aqueous EG surfaces, there are numerous coexisting conformations of stable EG and EG-water complexes. A blue shift of the CH2 symmetric stretch peak in the SFG spectra was observed with an increase in the water concentration. This change indicates that EG behaves as a hydrogen-bond acceptor when solvated by additional water molecules. This also suggests that, in aqueous solutions of EG, EG-EG aggregates are unlikely to exist. The experimental blue shift is consistent with the results from the computational studies.

Computer Simulation↗
PubMed2005

Non-Watson-Crick base pairing in RNA. quantum chemical analysis of the cis Watson-Crick/sugar edge base pair family.

Large RNA molecules exhibit an astonishing variability of base-pairing patterns, while many of the RNA base-pairing families have no counterparts in DNA. The cis Watson-Crick/sugar edge (cis WC/SE) RNA base pairing is investigated by ab initio quantum chemical calculations. A detailed structural and energetic characterization of all 13 crystallographically detected members of this family is provided by means of B3LYP/6-31G and RIMP2/aug-cc-pVDZ calculations. Further, a prediction is made for the remaining 3 cis WC/SE base pairs which are yet to be seen in the experiments. The interaction energy calculations point at the key role of the 2'-OH group in stabilizing the sugar-base contact and predict all 16 cis WC/SE base-pairing patterns to be nearly isoenergetic. The perfect correlation of the main geometrical parameters in the gas-phase optimized and X-ray structures shows that the principle of isosteric substitutions in RNA is rooted from the intrinsic structural similarity of the isolated base pairs. The present quantum chemical calculations for the first time analyze base pairs involving the ribose 2'-OH group and unambiguously correlate the structural information known from experiments with the energetics of interactions. The calculations further show that the relative importance and absolute value of the dispersion energy in the cis WC/SE base pairs are enhanced compared to the standard base pairs. This may by an important factor contributing to the strength of such interactions when RNA folds in its polar environment. The calculations further demonstrate that the Cornell et al. force field commonly used in molecular modeling and simulations provides satisfactory performance for this type of RNA interactions.

Base Pairing↗
PubMed2006

Ab initio dynamic study of the reaction of Cl2LaR (R=H, CH3) with H2.

In this paper, a comparison between "static" and "dynamic" determination of the thermodynamic (DeltarF degrees) and kinetic data (DeltarF#) for the reaction of Cl2LaR (R=H, CH3) and H2 is given. A difference is obtained in the case of the reaction between Cl2LaH and H2 and can be attributed to a failure of the "static" approach based on the harmonic approximation. The influence of the zero point energy correction is also analyzed but does not explain the 30% difference between the two calculated activation energies. The influence of the flatness of the potential energy surface around the transition state is proved as no such an effect is observed for the reaction of Cl2LaCH3 and H2.

Computer Simulation↗
PubMed2005

Computational and spectroscopic characterization of the molecular and electronic structure of the Pb(II)-quercetin complex.

The interactions of lead(II) ion with a polyhydroxylated flavonoid, the quercetin molecule, were investigated in methanol solution. The quercetin/metal stoichiometries and equilibrium stability constants for metal binding to quercetin have been determined by UV-vis spectroscopy combined with chemometrics methods. The 2:1, 1:2, and predominant 1:1 species are formed in solution. Among the three potential sites of chelation present in the quercetin structure, the catechol function presents the highest complexation power toward Pb(II), in opposition with previous results found for Al(III) complexation. This result has been confirmed by the good agreement of the experimental and theoretical features for both the electronic and vibrational spectra of the 1:1 complex. DT-DFT calculations show that the bathochromic shift of the long-wavelength band of the UV-vis spectra, that occurs upon complexation, is due to a ligand-to-metal charge transfer. The molecular structure of the ligand is not much modified by the coordination of lead at the level of the catecholate.

Computer Simulation↗