Molecular dynamics and Monte Carlo simulations for the structure of the aqueous trimethylammonium chloride solution in the 0.2-1 molar range

Molecular dynamics and Monte Carlo simulations have been performed for characterizing the structure of the 0.2 and 1 molar aqueous trimethylammonium chloride solutions. Atomic charges were derived through the CHELPG and RESP fits to the molecular electrostatic potentials calculated for the cation in water at the IEF-PCM/B3LYP level using the 6-31G* and 6-311++G** basis sets. Maxima and minima of the calculated radial distribution functions were not sensitive to the four atomic charge sets. Simulated solution structures suggest non-negligible solute-solute interactions and remarkable inhomogeneity at both concentrations. This means that equilibrium ratios, derived for conformers/tautomers by means of ab initio calculations with the IEF-PCM continuum dielectric solvent model, should be corrected for free energy changes following solute association when compared to experimental data obtained for the 0.1-1 molar aqueous solutions.     

Theoretical study of the enol imine <--> enaminone tautomeric equilibrium in organic solvents

The tautomeric enol imine <--> enaminone (phenol <--> quinone) equilibrium of the 1-hydroxy-2-naphthaldehyde Schiff base (2-phenyliminomethyl-naphthalen-1-ol) was investigated by density functional theory (B3LYP) and ab initio (MP2) methods in the IEF-PCM polarizable continuum dielectric solvent approximation and by a combined ab initio + FEP/MC study by considering an explicit solvent model. Special emphasis was put on the effect of solvation on this equilibrium by using an apolar (CCl4), polar aprotic (CH3CN), and polar protic (CH3OH) solvent. Compared with experimental tautomerization Gibbs free energies, the IEF-PCM/B3LYP calculations apparently overestimate the stability of the quinone form both when the 6-31G(d,p) and the 6-311++G(d,p) basis sets are applied. IEF-PCM/MP2 studies with the above basis sets predict the preference of the aromatic phenol tautomer, in contrast to the experiment in methanol and acetonitrile solvent. Calculation of the total relative free energy as DeltaG(tot) = DeltaE(int)(IEF-PCM/QCISD(T)/6-31G(d)) + DeltaG(solv, FEP/MC) + DeltaG(thermal) provided agreement with the experimental values up to 0.6 kcal/mol in the three solvents, and the predominant tautomer was always correctly predicted. In-solution relevant atomic charges, derived by a fit to the molecular electrostatic potential generated by the IEF-PCM/B3LYP/6-31G(d,p) wave function, show strong dependence on the fitting procedure (CHELPG or RESP) and are fairly insensitive to the chemical nature of the actual solvent. Use of the CHELPG charges in FEP/MC simulations revealed to be superior in comparison with the use of the RESP charge set.     

An ab initio MO study on the structures and electronic states of hydrogen-bonded O3- HF and SO2-HF complexes

Ab initio molecular orbital (MO) calculations have been carried out for base-hydrogen fluoride (HF) complexes (base = O3 and SO2) in order to elucidate the structures and energetics of the complexes. The ab initio calculations were performed up to the QCISD(T)/6-311++G(d,p) level of theory. In both complexes, hydrogen-bonded structures where the hydrogen of HF orients toward one of the oxygen atoms of bases were obtained as stable forms. The calculations showed that cis and trans isomers exist in both complexes. All calculations for the SO2-HF complex indicated that the cis form is more stable in energy than the trans form. On the other hand, in O3-HF complexes, the stable structures are changed by the ab initio levels of theory used, and the energies of the cis and trans forms are close to each other. From the most sophisticated calculations (QCISD(T)/6-311++G(d,p)//QCISD/6-311+G(d) level), it was predicted that the complex formation energies for cis SO2-HF, trans SO2-HF, cis O3-HF, and trans O3-HF are 6.1, 5.7, 3.4, and 3.6 kcal/mol, respectively, indicating that the binding energy of HF to SO2 is larger than that of O3. The harmonic vibrational frequencies calculated for cis O3-HF and cis SO2-HF complexes were in good agreement with the experimental values measured by Andrews et al. Also, the calculated rotation constants for cis SO2-HF agreed with the experiment.     

Theory, measurements, and modeling of OH and HO2 formation in the reaction of cyclohexyl radicals with O2

The production of OH and HO(2) in Cl-initiated oxidation of cyclohexane has been measured using pulsed-laser photolytic initiation and continuous-laser absorption detection. The experimental data are modeled by master equation calculations that employ new G2(MP2)-like ab initio characterizations of important stationary points on the cyclo-C(6)H(11)O(2) surface. These ab initio calculations are a substantial expansion on previously published characterizations, including explicit consideration of conformational changes (chair-boat, axial-equatorial) and torsional potentials. The rate constants for the decomposition and ring-opening of cyclohexyl radical are also computed with ab initio based transition state theory calculations. Comparison of kinetic simulations based on the master equation results with the present experimental data and with literature determinations of branching fractions suggests adjustment of several transition state energies below their ab initio values. Simulations with the adjusted values agree well with the body of experimental data. The results once again emphasize the importance of both direct and indirect components of the kinetics for the production of both HO(2) and OH in radical + O(2) reactions.     

Vibrational spectra and analysis of acetohydrazide CH3-CO-NH-NH2

The structural stability of acetohydrazide CH(3)-CO-NH-NH(2) was investigated by DFT-B3LYP and ab initio MP2 calculations with 6-311+G** basis set. The C-N rotational barrier in the molecule was calculated to be about 26 kcal/mol that suggested the planar sp(2) nature of the nitrogen atom of the central NH moiety. The N atom of the terminal NH(2) group was predicted to highly prefer the pyramidal sp(3) structure with an inversion barrier of about 7-8 kcal/mol. The molecule was predicted to have a trans-syn (N-H bond is trans with respect to CO bond and NH(2) moiety is syn to C-N bond) conformation as the lowest energy structure. The vibrational frequencies were computed at B3LYP level of theory and normal coordinate calculations were carried out for the trans-syn acetohydrazide. Complete vibrational assignments were made on the basis of normal coordinate analyses and experimental infrared and Raman data.     

Vibrational analyses of vinylsulfonamide CH2CHSO2NH2

The structure and conformational stability of vinylsulfonamide CH2CHSO2NH2 were investigated by DFT-B3LYP/6-311+G** and ab initio MP2/6-311+G** calculations. From the calculations the molecule was predicted to exist predominantly in the gauche-syn (vinyl group nearly eclipses one of the SO bonds and the NH2 and the SO2 moieties eclipse each other) conformation with the possibility of low abundance of the cis-syn and the gauche-anti forms. The asymmetric potential function for the internal rotation about CS bond was determined for the molecule. The vibrational frequencies were computed at DFT-B3LYP level for the gauche-syn conformer of the molecule and its d2(C2H3SO2ND2) and d3(C2D3SO2NH2) deuterated species. Normal coordinate calculations were then carried out and the potential energy distributions were calculated for the molecule.     

Mechanistic Study on the Monofunctional Binding of Hydrolysis Products of Non-planar Heterocyclic Complexes Trans-[PtCl_2NH_3（piperidine）] and Trans-[PtCl_2（piperidine）_2] to DNA Purine Bases

The monofunctional substitution reactions between trans-[PtCl(H2O)(NH3)(pip)]+,trans-[Pt(H2O)2(NH3)(pip)]2+,trans-[PtCl(H2O)(pip)2]+,trans-[Pt(H2O)2(pip)2]2+ (pip = piperidine) and adenine/guanine nucleotides are explored by using B3LYP hybrid functional and IEF-PCM salvation models. For the trans-[Pt(H2O)2(NH3)(pip)]2+ and trans-[PtCl(H2O)(NH3)(pip)]+ complexes,the computed barrier heights in aqueous solution are 13.5/13.5 and 11.6/11.6 kcal/mol from trans-Pt-chloroaqua complex to trans/cis-monoadduct for adenine and guanine,and the corresponding values are 20.7/20.7 and 18.8/18.8 kcal/mol from trans-Pt-diaqua complex to trans/cis-monoadduct for adenine and guanine,respectively. For trans-[PtCl(H2O)(pip)2]+ and trans-[Pt(H2O)2(pip)2]2+,the corresponding values are 21.5/21.3 and 19.4/19.4 kcal/mol,and 26.0/26.0 and 20.7/20.8 kal/mol for adenine and guanine,respectively. Our calculations demonstrate that the barrier heights of chloroaqua are lower than the corresponding values of diaqua for adenine and guanine. In addition,the free energies of activation for guanine in aqueous solution are all smaller than that for adenine,which predicts a preference of 1.9 kcal/mol when trans-[PtCl(H2O)(NH3)(pip)]+ and trans-[Pt(H2O)2(NH3)(pip)]2+ are the active agents and ～1.9 and ～ 5.3 kcal/mol when trans-[PtCl(H2O)(pip)2]+ and trans-[Pt(H2O)2(pip)2]2+ are the active agents,respectively. For the reaction of trans-Pt-chloroaqua (or diaqua) to cis-monoadduct,we obtain the same transition-state structure as from the reaction of trans-Pt-chloroaqua (or diaqua) to trans-monoadduct,which seems that the trans-Pt-chloroaqua (or diaqua) complex can generate trans-or cis-monoadduct via the same transition-state.     

Conformational stability, vibrational assignmenents, barriers to internal rotations and ab initio calculations of 2-aminophenol (d 0 and d3)

The Raman (3700-100 cm(-1)) and infrared (4000-400 cm(-1)) spectra of solid 2-aminophenol (2AP) have been recorded. The internal rotation of both OH and NH2 moieties produce ten conformers with either Cs or C1 symmetry. However, the calculated energies as well as the imaginary vibrational frequencies reduce rotational isomerism to five isomers. The molecular geometry has been optimized without any constraints using RHF, MP2 and B3LYP levels of theory at 6-31G(d), 6-311+G(d) and 6-31++G(d,p) basis sets. All calculations predict 1 (cis; OH is directed towards NH2) to be the most stable conformation except RHF/6-31++G(d,p) basis set. The 1 (cis) isomer is found to be more stable than 8 (trans; OH is away from the NH2 moiety and the NH bonds are out-of-plane) by 1.7 kcal/mol (598 cm(-1)) as obtained from MP2/6-31G(d) calculations. Aided by experimental and theoretical vibrational spectra, cis and trans 2AP are coexist in solution but cis isomer is more likely present in the crystalline state. Aided by MP2 and B3LYP frequency calculations, molecular force fields, simulated vibrational spectra utilizing 6-31G(d) basis set as well as normal coordinate analysis, complete vibrational assignments for HOC6H4NH2 and DOC6H4ND2 have been proposed. Furthermore, we carried out potential surface scan, to determine the barriers to internal rotations of NH2 and OH groups. All results are reported herein and compared with similar molecules when appropriate.     

Heat of formation for the CH3CH=NH2+ cation by photoionization mass spectrometry

The m/z 44 appearance energies for five primary amines have been measured by threshold photoionization mass spectrometry. Following an analysis of the thermochemistry associated with these unimolecular fragmentations, a value of 665.1 +/- 1.4 kJ mol(-1) is obtained for the 298 K heat of formation for the ethylidenimmonium cation (CH(3)CH=NH(2)(+)). When combined with high-level ab initio calculations, this results in absolute proton affinities of 906.4 +/- 2.7 and 909.2 +/- 2.8 kJ mol(-1) for the ethylidenimines E-CH(3)CH=NH and Z-CH(3)CH=NH, respectively.     

Intramolecular hydrogen-bonding interactions in 2-nitrosophenol and nitrosonaphthols: ab initio, density functional, and nuclear magnetic resonance theoretical study

Intramolecular hydrogen bonding (IHB) interactions and molecular structures of 2-nitrosophenol, nitrosonaphthols, and their quinone-monooxime tautomers were investigated at ab initio and density functional theory (DFT) levels. The geometry optimization of the structures studied was performed without any geometrical restrictions. Possible conformations with different types of the IHB of the tautomers were considered to understand the nature of the HB among these conformers. The effect of solvent on hydrogen bond energies, conformational equilibria, and tautomerism in aqueous solution were studied. Natural bond orbital analysis was performed to study the IHB in the gaseous phase and in aqueous medium. The NMR 1H, 13C, 15N, and 17O chemical shifts in the gaseous phase and in solution for the studied compounds were calculated using the gauge-including atomic orbitals approach implemented in the Gaussian 03 program package. The optimized geometrical parameters and 1H NMR chemical shifts are in good agreement with previous theoretical and experimental data.     

The Dinitramide Anion, N(NO(2))(2)(-)

The infrared and Raman spectra of the NH(4)(+), K(+), and Cs(+) salts of N(NO(2))(2)(-) in the solid state and in solution have been measured and are assigned with the help of ab initio calculations at the HF/6-31G and MP2/6-31+G levels of theory. In agreement with the variations observed in the crystal structures, the vibrational spectra of the N(NO(2))(2)(-) anion are also strongly influenced by the counterions and the physical state. Whereas the ab initio calculations for the free N(NO(2))(2)(-) ion indicate a minimum energy structure of C(2) symmetry, Raman polarization measurements on solutions of the N(NO(2))(2)(-) anion suggest point group C(1) (i.e., no symmetry). This is attributed to the very small (<3 kcal/mol) N-NO(2) rotational barrier in N(NO(2))(2)(-) which allows for easy deformation.     

Vibrational analyses of sulfamoyl halides NH2SO2X (X is F, Cl and Br)

The structural stability of sulfamoyl halides NH(2)-SO(2)X (X is F, Cl and Br) were investigated by DFT-B3LYP/6-311+G** and ab initio MP2/6-311+G** calculations. From the calculations the molecules were predicted to exist only in the anti (XS bond is anti with respect to nitrogen lone pair) conformation with the possibility of very low abundance of the syn (SO(2) and NH(2) groups eclipse each other) form of only the fluoride. The equilibrium constant for the syn<-->anti conformational conversion of sulfamoyl fluoride was calculated to be 0.0172 that corresponds to an equilibrium mixture of about 2% syn and 98% anti at 298.15K. The vibrational frequencies were computed at DFT-B3LYP level for the stable anti conformer of the d(0) and d(2) (ND(2)-SO(2)X) deuterated species of the three molecules. Normal coordinate calculations were then carried out and the potential energy distributions were calculated for the molecules.     

Structure of the HOOO radical in liquid water: a theoretical study.

The HOOO radical is supposed to play a role in ozone chemistry, both in the gas phase and aqueous media. We discuss the influence of the solvent on the electronic and geometrical structure of this radical using density functional and high-level ab initio calculations together with continuum, discrete, and discrete-continuum solvent models. Solute-solvent electrostatic interactions are shown to be fundamental, and lead to a noticeable stabilization of the radical, which should adopt a trans conformation in aqueous media. In fact, no energy minimum for the cis conformation is predicted in these conditions.     

离子簇合物HeN_2~+的电子光谱的从头算研究

本文报道了离子簇合物HeN2＋的电子光谱的从头算结果。在MCSCF／6－31G（d，p）水平上，对其基态进行了几何优化，用该构型．在SDC1／6－31（d，p）水平上计算了基态的总能量。用SDCI方法计算得到HeN2＋从基态到选择激发态的垂直跃迁能、振子强度、跃迁频率、辐射寿命以及Einstain系数。该结果可以较好的验证maier的实验。     

The electronic structure of 2-chloro-2′-deoxyadenosine (drug) studied by Cl-NQR spectroscopy and ab initio calculations

Electronic structure and conformation of 2-chloro-2′-deoxyadenosine (2CldAdo) and 2-chloroadenosine (2ClAde) have been studied by ³⁵Cl-NQR spectroscopy and ab initio calculations by the B3LYP/6-31G^* method.

The usefulness of NQR spectroscopy and ab initio calculations for the investigation of redistribution of electron density and structural changes in 2CldAdo and 2ClAde was assessed and a comparison of the electron distribution in the unsubstituted 2ClAde (monomer, dimer) and the substituted 2ClAdo was made.     

Density functional theory study on carbon dioxide absorption into aqueous solutions of 2-amino-2-methyl-1-propanol using a continuum solvation model

We used density functional theory (DFT) calculations with the latest continuum solvation model (SMD/IEF-PCM) to determine the mechanism of CO(2) absorption into aqueous solutions of 2-amino-2-methyl-1-propanol (AMP). Possible absorption process reactions were investigated by transition-state optimization and intrinsic reaction coordinate (IRC) calculations in the aqueous solution at the SMD/IEF-PCM/B3LYP/6-31G(d) and SMD/IEF-PCM/B3LYP/6-311++G(d,p) levels of theory to determine the absorption pathways. We show that the carbamate anion forms by a two-step reaction via a zwitterion intermediate, and this occurs faster than the formation of the bicarbonate anion. However, we also predict that the carbamate readily decomposes by a reverse reaction rather than by hydrolysis. As a result, the final product is dominated by the thermodynamically stable bicarbonate anion that forms from AMP, H(2)O, and CO(2) in a single-step termolecular reaction.     

Adsorption of NH(3) and H(2)O in acidic chabazite. Comparison of ONIOM approach with periodic calculations

The adsorption of NH(3) and H(2)O in acidic chabazite has been studied with the B3LYP method within the cluster approach (5T, 48T clusters) and the periodic approach adopting a Si/Al = 11/1 chabazite and a basis set of polarized double-zeta quality. The 5T cluster has been treated fully ab initio at the B3LYP level whereas the 48T cluster has been treated with the ONIOM2 scheme using B3LYP as the high level of theory and the MNDO, AM1, and HF/3-21G methods as low levels of theory. Periodic calculations show that the adsorption of NH(3) in acidic chabazite takes place through an ion pair (NH(4)(+)-CHA(-)) structure, the computed adsorption energy being -32 kcal/mol. The adsorption of H(2)O leads to a hydrogen bonded (H(2)O-HCHA) complex with the computed adsorption energy of -20 kcal/mol. All ONIOM combinations provide similar structures to those obtained with periodic calculations. Adsorption energies, however, are sensitive to the low level used, especially for NH(3). The ONIOM B3LYP:HF/3-21G method is the one that provides more satisfactory results. Present results show that, for larger zeolites, the ONIOM scheme can be successfully applied while drastically reducing the cost of a fully ab initio treatment.     

A theoretical study of the mechanism of the water-catalyzed HCl elimination reactions of CHXCl(OH) (X = H, Cl) and HClCO in the gas phase and in aqueous solution

A systematic ab initio investigation of the water-assisted decomposition of chloromethanol, dichloromethanol, and formyl chloride as a function of the number of water molecules (up to six) building up the solvation shell is presented. The decomposition reactions of the chlorinated methanols and formyl chloride are accelerated substantially as the reaction system involves additional explicit coordination of water molecules. Rate constants for the decomposition of chlorinated methanols and formyl chloride were found to be in reasonable agreement with previous experimental observations of aqueous phase decomposition reactions of dichloromethanol [CHCl(2)(OH)] and formyl chloride. For example, using the calculated activation free energies in conjunction with the stabilization free energies from the ab initio calculations, the rate constant was predicted to be 1.2-1.5 x 10(4) s(-1) for the decomposition of formyl chloride in aqueous solution. This is in good agreement with the experimental rate constant of about 10(4) s(-1) reported in the literature. The mechanism for the water catalysis of the decomposition reactions as well as probable implications for the decomposition of these chlorinated methanol compounds and formaldehydes in the natural environment and as intermediates in advanced oxidation processes are briefly discussed.