Gas-phase Ab Initio Calculations Research Articles

On the influence of dimerisation of lumiflavin in aqueous solution on its optical spectra – a quantum chemical study

The solvent effects on the photophysical and photochemical properties of lumiflavin are studied. By comparing different models for the aqueous environment including gas-phase ab-initio calculations, explicit solvation, continuum solvation model and QM/MM simulations the different aspects of solvation are singled out and analysed in detail. Dimerisation of flavins and its effects on the absorption and emission spectrum of flavins are studied using quantum chemical methods. The absorption and emission spectra of lumiflavin in water are compared to the properties of dimeric lumiflavin and to available experimental data.

The Nature of Cation-Anion Interactions in Magnetic Ionic Liquids as Revealed Using High-Pressure Fourier Transform Infrared (FT-IR) Spectroscopy.

Magnetic ionic liquids are a group of magneto-responsive compounds that typically possess high ionic conductivities and low vapor pressures. In spite of the general interest in these materials, a number of questions concerning the fundamental interactions among the ions remain unanswered. We used vibrational spectroscopy to gain insight into the nature of these interactions. Intramolecular vibrational modes of the ions are quite sensitive to their local potential energy environments, which are ultimately defined by cation-anion coordination schemes present among the ions. Ambient pressure Fourier transform infrared (FT-IR) spectroscopy indicates comparable interaction motifs for 1-ethyl-3-methylimidazolium tetrachloroferrate(III), [emim]FeCl4, and 1-ethyl-3-methylimidazolium tetrabromoferrate(III), [emim]FeBr4, magnetic ionic liquids. However, the vibrational modes of [emim]FeCl4 generally occur at slightly higher frequencies than those of [emim]FeBr4. These differences reflect different interaction strengths between the [emim]+ cations and or anions. This conclusion is supported by gas-phase ab initio calculations of single [emim]FeCl4 and [emim]FeBr4 ion pairs that show longer C-H···Br-Fe interaction lengths compared to C-H···Cl-Fe. Although the IR spectra of [emim]FeCl4 and [emim]FeBr4 are comparable at ambient pressure, a different series of spectroscopic changes transpire when pressure is applied to these compounds. This suggests [emim]+ cations experience different types of interaction with the anions under high-pressure conditions. The pressure-dependent FT-IR spectra highlights the critical role ligands attached to the tetrahalogenoferrate(III) anions play in modulating cation-anion interactions in magnetic ionic liquids.

Alkynyl Pyridinium Crystals for Terahertz Generation

AbstractThe design and synthesis of three organic nonlinear optical crystals is presented for terahertz (THz) generation that incorporates the optimal characteristics of known organic nonlinear optical crystals 4‐(4‐(dimethylamino)styryl)‐1‐methylpyridinium 4‐methylbenzenesulfonate (DAST) and 2‐(4‐hydroxy‐3‐methoxystyryl)‐1‐methylquinolinium 2,4,6‐trimethylbenzenesulfonate (HMQ‐TMS). The three crystals feature the 4‐((4‐(dimethylamino)phenyl)ethynyl)‐1‐methylpyridin‐1‐ium (4DEP) cation and three different anion combinations. Gas phase ab initio calculations of the cation show that 4DEP has a larger hyperpolarizability than cations from both DAST and HMQ‐TMS. To obtain the molecular packing needed for large nonlinear optical susceptibility and efficient THz generation, three anions are tested that result in noncentrosymmetric crystals: 4‐methylbenzenesulfonate, 3‐nitrobenzenesulfonate, and napthalene‐2‐sulfonate. After synthesis and crystallization, the crystal structure is characterized via X‐ray diffraction (XRD) analysis, and the relative THz generation efficiency for ideal crystals is predicted. 4DEP‐N2S shows a roughly 30% larger relative second‐order nonlinear optical susceptibility compared to HMQ‐TMS and DAST and, therefore, shows promise as a new advanced THz generation crystal.

A Polarizable Atomic Multipole-Based Force Field for Molecular Dynamics Simulations of Anionic Lipids.

In all of the classical force fields, electrostatic interaction is simply treated and explicit electronic polarizability is neglected. The condensed-phase polarization, relative to the gas-phase charge distributions, is commonly accounted for in an average way by increasing the atomic charges, which remain fixed throughout simulations. Based on the lipid polarizable force field DMPC and following the same framework as Atomic Multipole Optimized Energetics for BiomoleculAr (AMOEBA) simulation, the present effort expands the force field to new anionic lipid models, in which the new lipids contain DMPG and POPS. The parameters are compatible with the AMOEBA force field, which includes water, ions, proteins, etc. The charge distribution of each atom is represented by the permanent atomic monopole, dipole and quadrupole moments, which are derived from the ab initio gas phase calculations. Many-body polarization including the inter- and intramolecular polarization is modeled in a consistent manner with distributed atomic polarizabilities. Molecular dynamics simulations of the two aqueous DMPG and POPS membrane bilayer systems, consisting of 72 lipids with water molecules, were then carried out to validate the force field parameters. Membrane width, area per lipid, volume per lipid, deuterium order parameters, electron density profile, electrostatic potential difference between the center of the bilayer and water are all calculated, and compared with limited experimental data.

Medium effects on the 1,3-dipolar cycloaddition of pyridazinium dicyanomethanide with ethyl vinyl ketone in pure and mixed solvents from QM/MM simulations.

The 1,3-dipolar cycloaddition reaction between pyridazinium dicyanomethanide 1 and ethyl vinyl ketone (EVK) has been reported to be a concerted mechanism based on gas-phase ab initio calculations. Our current investigation of this 1,3-dipolar cycloaddition reaction in water, methanol, acetonitrile, H2O-CH3CN, and CH3OH-CH3CN mixtures using novel two-dimensional potentials of mean force (2-D PMF) calculations coupled to QM/MM simulations predicts an alternative free energy surface that supports a stepwise mechanism. The results for the kinetic effect are uniformly in close accord with experimental data and reflect a trigger point for the exponential rate rise in water-acetonitrile mixture. When methanol replaced water, the rate enhancements are more gradual, and there is no trigger point. Calculations in pure solvents and their mixtures at 25 °C and with pure water and acetonitrile at 37 °C indicate that the secondary bridging H-bonding from the first water molecules is necessary for the exponential rate enhancements, which is strong supported by the experimental results. This work provides new insight into solvent effects on 1,3-dipolar cycloaddition reaction.

An Angular Overlap Model for Cu(II) Ion in the AMOEBA Polarizable Force Field.

An extensible polarizable force field for transition metal ion was developed based on AMOEBA and the angular overlap model (AOM) with consistent treatment of electrostatics for all atoms. Parameters were obtained by fitting molecular mechanics (MM) energies to various ab initio gas-phase calculations. The results of parameterization were presented for copper (II) ion ligated to water and model fragments of amino acid residues involved in the copper binding sites of type 1 copper proteins. Molecular dynamics (MD) simulations were performed on aqueous copper (II) ion at various temperatures, as well as plastocyanin (1AG6) and azurin (1DYZ). Results demonstrated that the AMOEBA-AOM significantly improves the accuracy of classical MM in a number of test cases when compared to ab initio calculations. The Jahn-Teller distortion for hexa-aqua copper (II) complex was handled automatically without specifically designating axial and in-plane ligands. Analyses of MD trajectories resulted in a 6-coordination first solvation shell for aqueous copper (II) ion and a 1.8ns average residence time of water molecules. The ensemble average geometries of 1AG6 and 1DYZ copper binding sites were in general agreement with X-ray and previous computational studies.

Molecular origins of nonlinear optical activity in zinc tris(thiourea)sulfate revealed by high-resolution x-ray diffraction data andab initiocalculations

Structure-property relationships are established in the nonlinear optical (NLO) material, zinc tris(thiourea)sulfate (ZTS), via an experimental charge-density study, x-ray constrained wave-function refinement, and quantum-mechanical calculations. The molecular charge-transfer characteristics of ZTS, that are important for NLO activity, are topologically analyzed via a multipolar refinement of high-resolution x-ray diffraction data, which is supported by neutron diffraction measurements. The extent to which each chemical bond is ionic or covalent in nature is categorized by Laplacian-based bonding classifiers of the electron density; these include bond ellipticities, energy densities, and the local source function. Correspondingly, the NLO origins of ZTS are judged to best resemble those of organic NLO materials. The molecular dipole moment, ${\mathbit{\ensuremath{\mu}}}_{\mathbf{i}}$, and (hyper)polarizability coefficients, ${\mathbit{\ensuremath{\alpha}}}_{\mathbf{ij}}$ and ${\mathbit{\ensuremath{\beta}}}_{\mathbf{ijk}}$, are calculated from the experimental diffraction data using the x-ray constrained wave-function method. Complementary gas-phase ab initio quantum-mechanical calculations of ${\mathbit{\ensuremath{\mu}}}_{\mathbf{i}}$, ${\mathbit{\ensuremath{\alpha}}}_{\mathbf{ij}}$, and ${\mathbit{\ensuremath{\beta}}}_{\mathbf{ijk}}$ offer a supporting comparison. When taken alone, the experimental charge-density analysis does not fare well in deriving ${\mathbit{\ensuremath{\mu}}}_{\mathbf{i}}$, ${\mathbit{\ensuremath{\alpha}}}_{\mathbf{ij}}$, or ${\mathbit{\ensuremath{\beta}}}_{\mathbf{ijk}}$, which is not entirely surprising given that the associated calculations are only generally valid for organic molecules. However, by refining the x-ray data within the constrained wave-function method, the evaluations of ${\mathbit{\ensuremath{\mu}}}_{\mathbf{i}}$, ${\mathbit{\ensuremath{\alpha}}}_{\mathbf{ij}}$, and ${\mathbit{\ensuremath{\beta}}}_{\mathbf{ijk}}$ are shown to agree very well with those from ab initio calculations and show remarkable normalization to experimental refractive index measurements. The small differences observed between ab initio and x-ray constrained wave-function refinement results can be related directly to gas- versus solid-state phase differences. ${\mathbit{\ensuremath{\mu}}}_{\mathbf{i}}$ is found to be 28.3 Debye (gas phase) and 29.7 Debye (solid state) while ${\mathbit{\ensuremath{\beta}}}_{\mathbf{ijk}}$ coefficients are not only significant but are also markedly three dimensional in form. Accordingly, substantial octupolar as well as dipolar NLO contributions in ZTS are indicated, which challenges the traditional focus on dipolar NLO molecules. This evaluation of NLO properties and their relation to the molecular structure offers several ways by which ZTS may be more widely functionalized as a NLO material. More generally, this case study on ZTS demonstrates how experimental and computational techniques can be combined to understand NLO structure-property relationships, an important tool for the quantum-tailored molecular design of next-generation metalorganic NLO materials.

Implicit inclusion of atomic polarization in modeling of partitioning between water and lipid bilayers

We propose an effective and straightforward way of including atomic polarization in simulations of the partitioning of small molecules in inhomogenous media based on classical molecular dynamics with non-polarizable force fields. The approach presented here takes advantage of the relatively fast sampling of phase space obtained with additive force fields by adding the polarization effects afterwards. By using pre-polarized charges for the polar and non-polar phases together with a polarization correction term the effects of atomic polarization are effectively taken into account. The results show a clear improvement compared to using the more common setup with one set of charges obtained from gas phase ab initio calculations. It is shown that when proper measures are taken into account computer simulations with non-polarizable force fields are able to accurately determine water-membrane partitioning and preferential location of small molecules in the membrane interior. We believe that the approach presented here can be useful in rational drug design and in investigations of molecular mechanisms of anesthetic or toxic action.

Footprinting molecular electrostatic potential surfaces for calculation of solvation energies

A liquid is composed of an ensemble of molecules that populate a large number of different states, so calculation of the solvation energy of a molecule in solution requires a method for summing the interactions with the environment over all of these states. The surface site interaction model for the properties of liquids at equilibrium (SSIMPLE) simplifies the surface of a molecule to a discrete number of specific interaction sites (SSIPs). The thermodynamic properties of these interaction sites can be characterised experimentally, for example, through measurement of association constants for the formation of simple complexes that feature a single H-bonding interaction. Correlation of experimentally determined solution phase H-bond parameters with gas phase ab initio calculations of maxima and minima on molecular electrostatic potential surfaces (MEPS) provides a method for converting gas phase calculations on isolated molecules to parameters that can be used to estimate solution phase interaction free energies. This approach has been generalised using a footprinting technique that converts an MEPS into a discrete set of SSIPs (each described by a polar interaction parameter, εi). These SSIPs represent the molecular recognition properties of the entire surface of the molecule. For example, water is described by four SSIPs, two H-bond donor sites and two H-bond acceptor sites. A liquid mixture is described as an ensemble of SSIPs that represent the components of the mixture at appropriate concentrations. Individual SSIPs are assumed to be independent, so speciation of SSIP contacts can be calculated based on properties of the individual SSIP interactions, which are given by the sum of a polar (εiεj) and a non-polar (E(vdW)) interaction term. Results are presented for calculation the free energies of transfer of a range of organic molecules from the pure liquid into water, from the pure liquid into n-hexadecane, from n-hexadecane into water, from n-octanol into water, and for the transfer of water from pure water into a range of organic liquids. The agreement with experiment is accurate to within 1.6-3.9 kJ mol(-1) root mean square difference, which suggests that the SSIMPLE approach is a promising method for estimation of solvation energies in more complex systems.

SO2Capture by Guanidinium-Based Ionic Liquids: A Theoretical Study

Ionic liquids (ILs) show good performances in SO(2) separation science, e.g., SO(2) capture from high-temperature flue gas or separation from gas mixtures. In this work, the mechanism of capturing SO(2) by three guanidinium-based ILs, 1,1,3,3-tetramethylguanidinium lactate ([tmgHH][L]), 1,1,3,3-tetramethylguanidinium bis(trifluoromethylsulfonyl)imide ([tmgHH][Tf(2)N]), and 1,1,3,3-tetramethylguanidinium tetrafluoroborate ([tmgHH][BF(4)]), is investigated by using molecular dynamic simulation and ab initio calculation. The results of condensed phase molecular dynamic simulation for the mixtures of SO(2) and these three ILs indicate the similar SO(2) organization and interaction among them; SO(2) may organize around [tmgHH](+) while it favorably organizes around the anions through Lewis acid-base interaction. Gas phase ab initio calculations show that [tmgHH][L] chemically interacts with SO(2) while [tmgHH][Tf(2)N] and [tmgHH][BF(4)] do not, which is supported by the earlier FT-IR and (1)H NMR data and is also consistent with the experimental result of a much higher absorption capability of [tmgHH][L] for SO(2) than the latter two. The anion plays a key role in the chemical interaction between [tmgHH][L] and SO(2), the S atom is bonded to the N atom on -NH(2) of [tmgHH](+), and some products with aminosulfate or aminosulfinic acid fragment may be formed. This work shows that IL structures should be carefully tailored for their final application in SO(2) capture.

The molecular structure of 1,1-dichlorosilacyclopentane as obtained from gas-phase electron diffraction and ab initio calculations

The molecular structure of 1,1-dichlorosilacyclopentane (DCSCP) has been investigated by means of gas-phase electron diffraction and quantum mechanical calculation. We applied both a pseudorotation model to account for the dynamic and large amplitude motion in DCSCP, and a one-conformer model of C 1 symmetry. Using the computational results we analyzed the dependency of the ring geometrical parameters and vibrational mean amplitudes on the phase angle φ. The joint electron diffraction and ab initio study has led to the following r a structural parameters of DCSCP ( C 1 conformer): r(Si–Cl) = 2.047(2) Å, r(Si–C) = 1.867(4) Å, average r(C–C) ring = 1.548(4) Å, average r(C–H) = 1.103(7) Å, <(C–Si–C) = 97.4(6)°, <(Cl–Si–Cl) = 104.8(10)°, and effective phase angle φ = 74.8(58)°. The puckering amplitude for the five-membered ring was determined to be q = 0.480(24) Å. The quantum mechanical calculations were performed by utilizing the UHF, B3LYP, and MP2 methods in combination with basis sets 6-311++G(2df,2pd), 6-311++G(df,pd), 6-311++G(p,d), 6-311+G(d,p), 6-311G(d,p) and Dunning double and triple zeta (with and without augmentation). All these methods have consistently shown that the C 2 conformer is more stable than the C s symmetric form. For all calculations we used the MOLPRO and Gaussian03 packages. NBO and AIM analyses were also carried out to explore the bond/anti-bond hyperconjugative interactions and the topological properties of the charge density distribution in DCSCP. NBO scheme including second-order perturbation analysis has shown that the major orbital stabilizing interactions are between the chlorine lone pair ( n π) Cl and the low-lying σ Si – C2 ∗ and σ Si – C5 ∗ antibonding orbitals. It was found that remote σ Si–C → σ C – H ∗ interactions are stabilized by 4.4 kcal mol −1 and contribute to the stabilization of the C 2 conformer in DCSCP. Deletion analysis was performed using various deletion algorithms like NOSTAR, NOVIC, NOGEM (see text). The stabilization energy for the C 2 conformer resulting from the difference of the non-Lewis energy E(NL) C 2 – E(NL) Cs was 7.1 kcal mol −1. Similar analyses using the same quantum mechanical procedures mentioned above have been conducted to study silacyclopentane (SCP), 1,1-difluorosilacyclopentane (DFSCP), and 1,1-dibromosilacyclopentane (DBSCP).

Development of OPLS-AA Force Field Parameters for 68 Unique Ionic Liquids.

OPLS-AA force field parameters have been developed and validated for use in the simulation of 68 unique combinations of room temperature ionic liquids featuring 1-alkyl-3-methylimidazolium [RMIM] (R = Me, Et, Bu, Hex, Oct), N-alkylpyridinium [RPyr], and choline cations, along with Cl(-), PF6(-), BF4(-), NO3(-), AlCl4(-), Al2Cl7(-), TfO(-), saccharinate, and acesulfamate anions. The new parameters were fit to conformational profiles from gas-phase ab initio calculations at the LMP2/cc-pVTZ(-f)//HF/6-31G(d) theory level and compared to experimental condensed-phase structural and thermodynamic data. Monte Carlo simulations of the ionic liquids gave relative deviations from experimental densities of ca. 1-3% at 25 °C for most combinations and also yielded close agreement over a temperature range of 5 to 90 °C. Predicted heats of vaporization compared well with available experimental data and estimates. Transferability of the new parameters to multiple alkyl side-chain lengths for [RMIM] and [RPyr] was determined to give excellent agreement with charges and torsion potentials developed specific to desired alkyl lengths in 35 separate ionic liquid simulations. As further validation of the newly developed parameters, the Kemp elimination reaction of benzisoxazole via piperidine was computed in 1-butyl-3-methylimidazolium hexafluorophosphate [BMIM][PF6] using mixed quantum and molecular mechanics (QM/MM) simulations and was found to give close agreement with the experimental free energy of activation.

Multidimensional Exploration of Valley−Ridge Inflection Points on Potential-Energy Surfaces

The ene reaction between singlet oxygen ((1)O(2)) and simple alkenes has been reported as the first experimentally supported example of a potential-energy surface (PES) featuring a valley-ridge inflection that contributes to the selectivity of product formation (J. Am. Chem. Soc. 2003, 125, 1319-1328). That PES, based on gas-phase ab initio calculations and experimental kinetic isotope effects, has shaped the current (1)O(2) ene mechanism by advocating a concerted "two-step no-intermediate" mechanism. Our current investigation of the ene reaction between (1)O(2) and tetramethylethylene in water, DMSO, and cyclohexane using novel 3-dimensional potentials of mean force (3-D PMF) calculations coupled to QM/MM simulations predicts an alternative free-energy surface that supports a traditional stepwise mechanism interpretation featuring a symmetric charge-separated perepoxide intermediate. Solvent polarity dictates the stability of the intermediate and controls the activation barrier for ene product formation. Transformation of the higher order condensed-phase 3-D PMF potential-energy surface, computed following three simultaneous reaction coordinates, into a downgraded 2-D surface results in the "two-step no-intermediate" mechanism. CCSD(T) and MP4(SDQ) free-energy maps in DMSO, constructed from a 3-D grid of B3LYP geometries using the CPCM solvent model, reproduce the QM/MM results and confirm that when solvent is taken into account the gas-phase bifurcation reaction pathway converts into a stepwise mechanism. This manuscript provides new insight into the biologically and synthetically important (1)O(2) ene reaction and highlights a new multidimensional approach for constructing potential-energy surfaces.

N,N‐Dimethylaminopropylsilane: A Case Study on the Nature of Weak Intramolecular Si⋅⋅⋅N Interactions

N,N-Dimethylaminopropylsilane H(3)Si(CH(2))(3)NMe(2) was synthesised by the reaction of (MeO)(3)Si(CH(2))(3)NMe(2) with lithium aluminium hydride. Its solid-state structure was determined by X-ray diffraction, which revealed a five-membered ring with an SiN distance of 2.712(2) A. Investigation of the structure by gas-phase electron diffraction (GED), ab initio and density functional calculations and IR spectroscopy revealed that the situation in the gas phase is more complicated, with at least four conformers present in appreciable quantities. Infrared spectra indicated a possible SiN interaction in the Si-H stretching region (2000-2200 cm(-1)), as the approach of the nitrogen atom in the five-membered ring weakens the bond to the hydrogen atom in the trans position. Simulated gas-phase IR spectra generated from ab initio calculations (MP2/TZVPP) exhibited good agreement with the experimental spectrum. A method is proposed by which the fraction of the conformer with a five-membered ring can be determined by a least-squares fit of the calculated to experimental absorption intensities. The abundance of this conformer was determined as 23.7(6) %, in good agreement with the GED value of 24(6) %. The equilibrium SiN distance predicted by theory for the gas-phase structure was highly variable, ranging from 2.73 (MP2) to 3.15 A (HF). The value obtained by GED is 2.91(4) A, which could be confirmed by a scan of the potential-energy surface at the DF-LCCSD[T] level of theory. The nature of the weak dative bond in H(3)Si(CH(2))(3)NMe(2) can be described in terms of attractive inter-electronic correlation forces (dispersion) and is also interpreted in terms of the topology of the electron density.

Indirect spin–spin coupling constants in CH 4, SiH 4 and GeH 4 – Gas-phase NMR experiment and ab initio calculations

New values of the indirect spin–spin coupling constants in CH 4, SiH 4 and GeH 4, derived from experiment and ab initio calculations, are reported. The new experimental values of 1 J(CH), 1 J(SiH) and 1 J(GeH) are obtained from gas-phase NMR spectra. The dependence of the measured one-bond coupling constants on the density is analysed and the results are extrapolated to zero-density point to eliminate the effects due to intermolecular forces. In the calculation of the coupling constants, at the nonrelativistic level coupled cluster singles and doubles (CCSD) perturbation theory is used and the basis set convergence of the results is discussed. The relativistic corrections are estimated from Dirac–Hartree–Fock (DHF) calculations. The final theoretical values are obtained adding available estimates of the vibrational and temperature corrections. The agreement of the calculated and experimental 1 J(XH), X = C, Si, Ge, constants is very satisfying, the differences are approximately 1–3%.

Dimethylalkoxygallane incorporating a donor-functionalised alkoxide: the monomeric gas-phase structure

The structure of the vapour produced upon heating the dimethylalkoxygallane [Me(2)GaOCH(2)CH(2)NMe(2)](2) has been studied by gas-phase electron diffraction and ab initio molecular orbital calculations; only the monomeric form [Me(2)GaOCH(2)CH(2)NMe(2)] is observed in the vapour, with the nitrogen atom forming a dative bond with the metal centre.

Molecular structures of M(But)3(M = Al, Ga, In) using gas-phase electron diffraction and ab initio calculations: experimental and computational evidence for charge-transfer processes leading to photodissociation

The gas-phase structures of AI(Bu')3 and Ga(Bu')3 have been investigated by electron diffraction and are shown to consist of monomeric units with very slightly pyramidal geometries. Salient structural parameters (r(hl)) include r(A1-C) = 2.008(2) A and r(Ga-C) = 2.032(2) A. For both compounds the ligand orientations and geometries are controlled by interligand interactions. The structures of M(Bu(t))3 (M = Al, Ga, In) have been calculated ab initio and those for the aluminium and gallium derivatives are in good agreement with the electron-diffraction structures. Comparison of the ab initio calculated structure of In(Bu')3 with those of Al(Bu(t))3 and Ga(Bu(t))3 suggests that the significantly different photochemistry exhibited by the former does not result from structural factors. In fact the compounds undergo a charge-transfer process in the UV region, with the wavelength required calculated to be slightly longer for the indium compound than for the other two.

The application of cluster analysis to identify conformational preferences in enones and enimines from crystal structural data

Cluster analysis can be an effective tool for analysing large quantities of data. Here it has been applied to the conformational analysis of enones and enimines in the crystalline solid state, using structural information mined from the Cambridge Structural Database. The forms that are common in the gaseous state and in solution are already known from spectroscopic studies. These forms are also found to be the most common conformations observed in the solid state; however, the clustering method highlights those structures that do not conform to the expected geometries. The study is supported by ab initio gas phase calculations on simple enone and enimine fragments.

Towards accurate solvation dynamics of divalent cations in water using the polarizable amoeba force field: From energetics to structure

Molecular dynamics simulations were performed using a modified amoeba force field to determine hydration and dynamical properties of the divalent cations Ca2+ and Mg2+. The extension of amoeba to divalent cations required the introduction of a cation specific parametrization. To accomplish this, the Thole polarization damping model parametrization was modified based on the ab initio polarization energy computed by a constrained space orbital variation energy decomposition scheme. Excellent agreement has been found with condensed phase experimental results using parameters derived from gas phase ab initio calculations. Additionally, we have observed that the coordination of the calcium cation is influenced by the size of the periodic water box, a recurrent issue in first principles molecular dynamics studies.

Molecular structure, conformation, potential to internal rotation, and ideal gas thermodynamic properties of 3-fluoroanisole and 3,5-difluoroanisole as studied by gas-phase electron diffraction and quantum chemical calculations

3-Fluoroanisole (3-FA) and 3,5-difluoroanisole (3,5-DFA) have been studied by gas-phase electron diffraction, ab initio (HF and MP2), and density functional theory (B3LYP) calculations. Both molecules have a planar heavy atom skeleton. 3,5-DFA exists as a single conformer of C s symmetry, whereas 3-FA exists as a mixture of two planar conformers of C s symmetry with the syn form (the O–CH 3 bond is oriented toward the fluorine atom) being 0.1–0.2 kcal/mol lower in energy than the anti form (the O–CH 3 bond is oriented away from the fluorine atom). From the experimental scattering intensities the following geometric parameters ( r a distances and ∠ α angles with 3σ uncertainties) were derived for 3,5-DFA: r(C–C) av=1.391(2) Å, r(C Ph–O)=1.359(13) Å, r(C Me–O)=1.427(19) Å, r(C–F) av=1.350(6) Å, ∠C–C–C=116.0–123.6°, ∠C–O–C=118.7(12)°, ∠C2–C1–O=114.9(10)°, ∠C6–C1–O=124.9(10)°, ∠(C–C–F) av=118.4(17)°, and for 3-FA, syn conformer: r(C–C) av=1.393(3) Å, r(C Ph–O)=1.364(13) Å, r(C Me–O)=1.423(14) Å, r(C–F)=1.348(9) Å, ∠C–C–C=117.7–123.1°, ∠C–O–C=118.4(11)°, ∠C2–C1–O=124.7(17)°, ∠C6–C1–O=115.1(17)°, ∠C2–C3–F=118.0(24)°. The mole fractions of the syn and anti conformers were found to be 0.55(17) and 0.45, respectively, in good agreement with the theoretical prediction. Ideal gas thermodynamic functions, S°( T), C p ° ( T ) , H°( T)− H°(0), for anisole, 3-FA, and 3,5-DFA were obtained on the basis of B3LYP calculations. Enthalpies of formations, Δ f H 298 ° , were calculated using a Gaussian-3X (G3X) method and the method of isodesmic reactions. Calculated values of C p ° ( T ) and Δ f H 298 ° for anisole are in good agreement with experimental data.