The intermolecular structure of phosphoric acid-N,N-dimethylformamide mixtures as studied by computer simulation

The computer simulation of H(3)PO(4)-N,N-dimethylformamide (DMF) mixtures over the whole concentration range using molecular dynamic (MD) methods has been carried out. The preferential orientations of the nearest neighbors of H(3)PO(4) and DMF molecules were obtained using the ranked radial distribution functions technique. On the basis of MD results, the parameters of hydrogen bonds between molecules in mixture were calculated. The changes of the intermolecular structure of mixture as a function of acid composition over the whole concentration range were analyzed and reported. Analysis of O···H distance distributions and angles between O-H (H(3)PO(4)) and C=O (DMF) or P=O (H(3)PO(4)) vector distributions showed that O(DMF) and O(H(3)PO(4)) may each have two hydrogen bonds.     

Dimer form of 1,3-dimethyluracil studied by the AM1 semiempirical method

A study of the dimer form of 1,3-dimethyluracil was carried out. The optimum geometric parameters in the monomeric and dimeric forms were obtained using the AM 1 semiempirical method. The results were compared with those reported by X-ray diffraction. The energies in the dimer formation and in the intramolecular C? H···O interaction were calculated. Electronic density maps in two and three dimensions were drawn. Several calculated thermodynamic parameters are discussed. © 1994 John Wiley & Sons, Inc.     

Hydration of small anions: Calculations by the AM1 semiempirical method

The AM1 semiempirical molecular orbital method has been used to calculate successive heats of hydration of small anions, including hydride, hydroxide, and the halogen ions, for cluster sizes up to 11 water molecules surrounding the central anion. Heats of hydration agree with available experimental data to within a few kcal/mol. Structures, however, do not always agree well with available ab initio calculations on clusters with one or two water molecules. The results indicate that the AM1 semiempirical technique applied to finite-sized clusters must be used with caution in understanding how hydration affects the chemical reactions of anions.     

Study of the thermal decomposition of 3-cyclopentenone by using the AM1 semiempirical method

Summary RHF/AM1 and UHF/AM1 low-dimensionality surfaces were calculated by applying the reaction-coordinate technique to the thermal decomposition of 3-cyclopentenone. Several stationary points were accurately located within the entire coordinate space. Although the two formalisms used predicted asynchronous reaction pathways for the process, our results illustrate the limitations of single reference treatments of two-bond reactions while the nature of the reaction path remains uncertain.     

A study of photoelectron spectra in the framework of the semiempirical AM1 method

The characteristics of photoelectron (PE) spectra of 2-phenylpyrroles and biphenyls have been correlated with the UV spectroscopy data for their radical cations. The geometric and electronic structures of the compounds and radical cations have been calculated using the AM1 method. The absorption bands of the radical cations observed in the visible region of spectrum have been found to pertain to the quasi-Koopmans type,i.e., they are realized between the doubly and partially occupied -MO, but their energies differ strongly from those calculated on the basis of PE spectra. This is explained by the distinction between the spatial structure of a molecule and that of the respective radical cation. The second cause of the discrepancy between the data of the two spectral methods consists in orbital — interactions, which are most conspicuous in the case of 4(4)-halogen-substituted compounds.For Part 4 see ref. 1.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 5, pp. 869–874, May, 1993.     

Vibrational Stark effect: Theoretical determination through the semiempirical AM1 method

The vibrational Stark effect of a series of small molecules has been calculated by means of the semiempirical AM1 method through addition of the electron–field interaction term in the one-electron Hamiltonian. Optimized geometrical parameters along with harmonic frequencies and line intensities are determined for different strengths of the applied uniform electric field. The perturbed spectra are compared with theoretical studies carried out at the ab initio level and with experimental results. The vibrational Stark effect of the retinal molecule is also computed, showing that this kind of study is feasible in systems of biochemical interest. © 1992 by John Wiley & Sons, Inc.     

Simulating the proton transfer in gramicidin A by a sequential dynamical Monte Carlo method

The large interest in long-range proton transfer in biomolecules is triggered by its importance for many biochemical processes such as biological energy transduction and drug detoxification. Since long-range proton transfer occurs on a microsecond time scale, simulating this process on a molecular level is still a challenging task and not possible with standard simulation methods. In general, the dynamics of a reactive system can be described by a master equation. A natural way to describe long-range charge transfer in biomolecules is to decompose the process into elementary steps which are transitions between microstates. Each microstate has a defined protonation pattern. Although such a master equation can in principle be solved analytically, it is often too demanding to solve this equation because of the large number of microstates. In this paper, we describe a new method which solves the master equation by a sequential dynamical Monte Carlo algorithm. Starting from one microstate, the evolution of the system is simulated as a stochastic process. The energetic parameters required for these simulations are determined by continuum electrostatic calculations. We apply this method to simulate the proton transfer through gramicidin A, a transmembrane proton channel, in dependence on the applied membrane potential and the pH value of the solution. As elementary steps in our reaction, we consider proton uptake and release, proton transfer along a hydrogen bond, and rotations of water molecules that constitute a proton wire through the channel. A simulation of 8 mus length took about 5 min on an Intel Pentium 4 CPU with 3.2 GHz. We obtained good agreement with experimental data for the proton flux through gramicidin A over a wide range of pH values and membrane potentials. We find that proton desolvation as well as water rotations are equally important for the proton transfer through gramicidin A at physiological membrane potentials. Our method allows to simulate long-range charge transfer in biological systems at time scales, which are not accessible by other methods.     

Investigation of UV spectra of isomeric nitropyrazoles by the semiempirical AM1 (CI) method

The absorption bands in the UV spectra of isomeric nitropyrazoles were assigned by the calculations in the semiempirical AMI (CI) approximation. The long-wave absorption of nitropyrazoles is caused by π→π* and η₀→π* transitions. The charge-transfer band is the most intense. The π→π* transitions undergo a considerable bathochromic shift in the deprotonation. The first ionization potential (PI) of the 4-nitropyrazole anion was estimated from the empirical dependence of the energy of the excited π-state on PI of alkyl-substituted 4-nitropyrazoles. The PI of the 4-nitropyrazole anion is 3 eV lower than that of a neutral molecule. This is evidence for a substantial destabilization of the boundary β-orbital in the heterolytic cleavage of the N−H bond. The analysis of the UV and NMR spectra of 3(5)-nitropyrazole confirms the viewpoint that the 3-nitro tautomer predominates in solution. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya. No. 2, pp. 310–314, February, 1997.     

A study by Raman spectroscopy and the semiempirical AM1 method on several 1,2-dihydroxybenzene solutions

The Raman spectra of 1,2-dihydroxybenzene (catechol) dissolved in six different compounds have been obtained and, on the basis of frequencies and depolarization ratios, the relevant structure of the solute has been inferred in every case. In addition, rotational barrier calculations using the AMI semiempirical method have been performed on several catechol—solvent systems. The theoretical results were in accord with experimental data and were related to structural properties of the solvents.     

AM1 semiempirical computational analysis of the homopolymerization of spiroorthocarbonate

Spiroorthocarbonates (SOCs) are monomers that have been shown to expand when homopolymerized. SOCs are potential monomer systems that can be combined with other monomers such as epoxy resin to produce a non-shrinking dental matrix for dental composites. The purpose of this study was to use a computer model (AM1) to study possible homopolymerization pathways for several SOC monomers. The gas phase transition states of three feasible reaction mechanisms for the homopolymerization of four spiroorthocarbonate 1,5,7,11-tetraoxaspiro[5,5]undecane (TOSU) systems have been examined using the AM1 semiempirical quantum mechanical model. In addition to the base TOSU noted above, the 2,8-dimethyl, 2,4,8,10-tetramethyl, and the 3,3,9,9-tetramethyl analogs were used in this study. The results of these calculations produced the heats of reaction, activation enthalpies and transition state structures. Our calculations indicate stabilization of the transition states by electron-donating and resonance-stabilizing substituent groups. The energies of activation of all of these systems were between 24 and 38 kcal/mol and all reactions were endothermic. Further, we found that there was a significant intermolecular attraction between TOSU monomers (≈3.5 kcal/mol). When compared with experimental studies of methylated TOSU by Sakai and co-workers, our calculations agree with the preferred site of nucleophilic attack, but not with the experimental rate results. It was concluded that the homopolymerization of the unsubstituted TOSU and its derivatives studied was endothermic and that the rate of homopolymerization of TOSU depends on an intermolecular pre-association of TOSU monomer in the condensed phase.     

Interpretation of photoelectron spectra in the AM1 semiempirical method. 3. 2-Substituted benzimidazoles

Analysis of photoelectron spectra of 2-substituted benzimidazoles showed that their orbital structure is determined by the form and energy position of the fragment orbital (-symmetry) of the substituent.For previous communication, see [1].Irkutsk Institute of Organic Chemistry, Siberian Branch, Russian Academy of Sciences, Irkutsk 664033. Translated from Izvestiya Akademii Nauk, Seriya Khimicheskaya, No. 4, pp. 880–884, April, 1992.     

Valence-bond calculations on ZNO and HGO using integrals computed through the semiempirical AM1 method

Valence-bond calculations have been carried out on ZnO and HgO using a basis set of Slatertype atomic orbitals and the one- and two-electron integrals as computed in the semiempirical AM 1 molecular orbital method. The zero differential overlap approximation has been used to calculate integrals between atomic orbital Slater determinants using the rules for matrix elements between determinants formed by orthogonal orbitals. Diabatic and adiabatic curves have been analyzed for the two systems, and results compared with molecular orbital AM 1 results. © 1992 John Wiley & Sons, Inc.     

Interpretation of photoelectron spectra within the framework of the AM1 semiempirical method. 2. Pyridines

Analysis of the orbital structure of isomeric pyridines carried out using photoelectron spectroscopy and the AM1 (GF) method showed that this structure is independent of the nature of the substituent at C ²⁽⁶⁾ and C ³⁽⁵⁾ : <n<. All the possible sequences of the highest occupied MO of different symmetry (, ) are realized for 4-substituted pyridines.For previous communication, see [1].Irkutsk Institute of Organic Chemistry, Siberian Branch, Russian Academy of Sciences, Irkutsk 664033. Translated from Izvestiya Akademii Nauk, Seriya Khimicheskaya, No. 4, pp. 872–880, April, 1992.     

An AM1 semiempirical study of host-guest complexation in hemicarcerand complexes

Semiempirical AM1 calculations have been carried out on host-guest complexes of model hemicarcerands 1a and 2a. The justification for the choice of the AM1 Hamiltonian was based on a comparison between reported X-ray data for the smaller tetrabromocavitand 4a and computational results obtained using several different Hamiltonians. The complexation behavior of hemicarcerands 1a and 2a have been compared with experimental results reported by Cram et al. for the related hemicarcerands 1b and 2b. Based on this comparison, a criterion for predicting guest encapsulation was developed, E(complexation), which relies on the calculation of AM1 heats of formation for host, guest, and hemicarceplex. If E(complexation) is lower than 10 kcal/mol, then a guest will be encapsulated, while if it is greater than 30 kcal/mol, a guest will not be encapsulated. The use of constrained-path AM1 optimizations to determine the energy barriers to guest entry and exit from the host was found to be a useful tool for examining suitable host-guest combinations when the E(complexation) criteria does not hold. We have computed the barriers to exit of N, N-dimethylformamide (dmf) and furan from the hemicarcerand 1a, the former has been compared with the experiment and shows excellent agreement. Based on the success of the above computational methods in predicting which host-guest combinations will form stable hemicarceplexes we have synthesized a new target hemicarceplex 1b.furan.     

A comparative AM1 and ab initio study of the intramolecular proton transfer in tautomeric organic compounds

The proton-transfer barriers along the intramolecular hydrogen bond in a series of substituted salicylaldehyde anils were calculated using the AM1 SCF semiempirical method. The reliability of this method for the calculation of proton-transfer barriers was analyzed by the comparison of AM1 barriers for a series of different tautomeric organic compounds with those calculated using ab initio SCF and second-order perturbation theory with extended basis sets. In general, the AM1 method systematically overestimates the barrier height. However, this error is approximately constant for given pairs of groups involved in the intramolecular proton transfer. © 1996 John Wiley & Sons, Inc.     

Parametrization in the AM 1 method

Parameter definition is considered for the AM 1 method, which is a new modification of MNDO incorporating better correction for atomic-core repulsion, so the promising approach can be used to calculate energy and structural characteristics for molecules and adducts. Calculations have been performed on heats of formation, ionization potentials, and dipole moments for various compounds, as well as structure parameters (bond lengths and bond and torsion angles), which are close to the standard ones and reproduce experimental values satisfactorily.Translated from Teoreticheskaya i Éksperimental'naya Khimiya, Vol. 24, No. 6, pp. 713–717, November–December, 1988.     

Thermochemistry of ethyl acetate solvation in the 1-octanol-N,N-dimethylformamide system

The thermal effects of ethyl acetate (EtOAc), 1-octanol (OctOH), and N,N-dimethylformamide (DMF) solution in a OctOH-DMF model system were measured using a calorimeter of variable temperature with an isothermal shell at 298 K. The standard enthalpies of solution and ester transfer from an alcohol to a binary mixture, and partial mole enthalpies of mixed solvent components were determined. The state of non-electrolyte molecules in OctOH-DMF and OctOH-DMF-EtOAc systems were studied using extended coordination model. It was found that the binary solvent is subjected to microclusterization, since the fraction of the single-type molecules in the solvation sphere of both components of a mixture is significantly higher than in the liquid phase volume. The conclusion was drawn that in the triple system, the ethyl acetate solvation sphere in the whole range of compositions is significantly enriched with amide owing to stronger esteramide dipole-dipole interaction.     

The electrochemical reaction of nitrate in N,N-dimethylformamide

Polarography, cyclic voltammetry and controlled-potential coulometry were used to study N,N-dimethylformamide solutions of nitrate. Nitrate is reversibly reduced in a one-electron step to NO(2). The diffusion coefficient of nitrate was polarographically estimated to be 4.6 x 10(-6) cm(2)/sec. Polarography in dimethylformamide was found to be a convenient method of analysis for nitrate in a solid fertilizer.     

Theoretical study of the proton affinities of 2-, 3-, and 4-monosubstituted pyridines in the gas phase by means of MINDO/3, MNDO,and AM1

Proton affinities (PAs) of 2-, 3-, and 4-monosubstituted pyridines in the gas phase are calculated using the MINDO/3, MNDO, and AM1 methods. The following substituents are considered: F, Cl, CN, CH₃, CF₃, CHO, NO₂, NH₂, N(CH₃)₂, OCH₃, and SCH₃. The results are compared with experimental values. It is found that all MINDO/3 PAs are ca. 6% too high (mean value) compared to the experimental results; on the other hand, the MNDO values are ca. 7% too low (mean value). However, a much better agreement has been observed for the AM1 method where the theoretical values are only ca. 2.4% too low (mean value). Correlations between the calculated proton affinities on one hand and the charges on the acid H atom and Hammett constants on the other hand are studied. Particularly good linear relationships are found for the 4-monosubstituted compounds within the AM1 formalism.     

Theoretical study of the reaction mechanism of proton transfer in glycinamide

To investigate the tautomerism of glycinamide that is induced by proton transfer, we present detailed theoretical studies on the reaction mechanism of both the isolated gas phase and H₂O‐assisted proton transfer process of glycinamide, using density functional theory calculations by means of the B3LYP hybrid functional. Twenty‐six geometries, including 10 significant transition states, were optimized, and these geometrical parameters are discussed in detail. The relative order of the activation energy for hydrogen atom transfer of all the conformers has been systematically explored in this essay. For the amido hydrogen atom transfer process, the relative order of the activation energy is: IV < II < III < I, while in the carbonic hydrogen atom transfer process, the relative order is IV > II > III > I. Meanwhile, the most favorable structure for both the amido hydrogen atom transfer and the carbonic hydrogen atom transfer has been found. The involvement of the water molecule not only can stabilize the transition states and the ground states, but can also reduce the activation energy greatly. The superior catalytic effect of H₂O has been discussed in detail. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006