Gas-phase Ab Initio Calculations Research Articles

A study of the asymmetry of ligands in bis(trichlorosilyl)tert-butylphosphine, PBut(SiCl3)2: molecular structure by gas-phase electron diffraction and ab initio calculations

The molecular structure of bis(trichlorosilyl)tert-butylphosphine has been determined in the gas phase by electron diffraction (GED) and high level ab initio molecular-orbital calculations. The C1 global minimum on the potential energy surface could be reached by twisting all three groups in the same sense by 15–20° from the fully staggered Cs conformation, found to be a saddle point and 26.7 kJ mol−1 higher in energy at HF/6-31G*. Important structural parameters (ra) are: (distances) P–C 190.6(6), P–Si (mean) 221.0(5), C–C (mean) 156.5(6) and Si–Cl (mean) 203.2(1) pm; (bond angles) P–C–C (mean) 109.7(6), C–P–Si 105.0(7) and 104.5(7), Si–P–Si 99.9(6), and P–Si–Cl (mean) 111.2°; (dihedral angles) Si(7)–P–C–C 87.0(17), Si(8)–P–C–C 168.3(17), Cl(17)–Si–P–C 68.3(17) and Cl(18)–Si–P–C 80.0(10)°. Theoretical predictions at the MP2(fc)/6-31G* level were used to restrain some of the refining parameters using the SARACEN method. The angles at silicon and carbon (tert-butyl) were found to vary from 105.9(7) to 117.4(5)°, indicating that the three groups are greatly distorted from regular tetrahedral geometry. The axial and equatorial components of the tilts of these groups have been investigated and the tert-butyl group was found to tilt in the direction of the phosphorus lone pair with virtually no equatorial tilt. One SiCl3 group is tilted towards the tert-butyl group and one tilted away, both with axial and equatorial components. The structures of the related molecules PBut(SiH3)2 and PBut(SiH3)(SiCl3) have also been investigated by ab initio calculations and the distortions analysed in a similar manner to those of PBut(SiCl3)2.

An alternative explanation for the catalytic proficiency of orotidine 5'-phosphate decarboxylase.

Orotidine 5'-phosphate decarboxylase (ODCase) is the most proficient enzyme known, enhancing the rate of decarboxylation of orotidine 5'-phosphate (OMP) by a factor of 10(17), which corresponds to a DeltaDeltaG++ of approximately 24 kcal/mol. Ground-state destabilization through local electrostatic stress has been recently proposed as the basis of catalytic rate enhancement for a mechanism that is the same as in solution. We have carried out gas-phase ab initio quantum mechanical calculations combined with a free energy method, a continuum solvent model, and molecular dynamics simulations to assess an alternative mechanism. Although we are not able to reproduce the experimentally observed DeltaDeltaG++ quantitatively, we present evidence that this DeltaDeltaG++ is very large, in the range found experimentally. We thus conclude that the preferred mechanism may well be different from that in solution, involving an equilibrium pre-protonation of OMP C5 by a catalytic lysine residue that greatly reduces the barrier to subsequent decarboxylation.

Hexachloroacetone (Cl3C–C([dbnd]O)–CCl3): conformational structure, and the matter of C2 equilibrium symmetry, reinvestigated by gas-phase electron diffraction and ab initio molecular orbital calculations

The molecular and conformational structure of hexachloroacetone, Cl3C–CO–CCl3, has been studied using gas-phase electron diffraction (GED) data at a temperature of 300°C, and ab initio molecular orbital calculations. The title compound exists in the gas phase as a single conformer with C2 symmetry, with a twist angle about the C–CCl3 bonds of τ=31.6 (12)° obtained from a quartic potential function tracing the A mode of torsional motion. Some structural parameter values obtained from the dynamic model GED refinements, using results from the theoretical calculations as constraints, are as follows (torsional vibrational average values with estimated 2σ uncertainties): Bond lengths (rg): r(C–C)=1.590 (10) Å, r(CO)=1.202 (11) Å, r(C–Cl)=1.772 (3) Å (average value of the three different C–Cl bonds). Bond angles (∠α): ∠ CCC=123.5 (11)°, ∠CCl=109.5 (3)° (average value of the three different CCCl angles), ∠CCO=118.2 (5)°. Scaled harmonic vibrational force fields were obtained at the HF/6-31G(d) level of theory, and used to calculate shrinkage corrections for all pseudoconformers in the GED dynamic model refinements. The value for the C2v potential barrier (V0=5.17kcalmol−1) in the quartic potential function was obtained from thermal- and zero-point-energy corrected MP2/6-311+G(2d) calculations. The results are discussed and compared with the results for some similar molecules.

The molecular structure of 2-bromostyrene and (E)β-bromostyrene obtained by gas-phase electron diffraction and ab initio molecular orbital calculations

The molecular structures of 2-bromostyrene (C6H4Br–CHCH2) and (E)β-bromostyrene (C6H5–CHCHBr) have been studied using gas-phase electron diffraction at 378 and 373K, respectively, together with ab initio molecular orbital calculations (HF/6-311G(d) and MP2/6-311G(d)). The experimental data for 2-bromostyrene are consistent with a non-planar model in which the vinyl group is rotated away from the bromine atom (τ(C8C7–C1–C2)≈155°). The presence of a small amount of a second conformer (τ(C8C7–C1–C2)≈54°) cannot be excluded. The ab initio calculations show the latter conformer to be a stable form, but 2.52kcal/mol higher in energy (MP2/6-311G(d)). The principle bond distances and valence angles obtained from least squares refinements of the electron-diffraction data are (rg and ∠α with 2σ uncertainties, including estimates of systematic errors and correlation in the experimental data): 〈r(C–H)〉=1.109 (13)Å (average value), r(C7C8)=1.328 (21)Å, 〈r(C–C)ph〉=1.405 (3)Å, r(C1–C7)=1.478 (11)Å, r(C2–Br)=1.913 (6)Å, ∠Br–C2–C3=117.2 (5)°, ∠C1–C7C8=130(4)°, ∠C7–C1–C2=122(1)° and τ(C8C7–C1–C2)=152 (20)°. (E)β-bromostyrene also exists in a non-planar form with the vinyl group rotated about 40° out of the plane of the phenyl group. The principle bond distances and angles (rg and ∠α) are: 〈r(C–H)〉=1.080(13)Å, r(C7C8)=1.344 (23)Å, 〈r(C–C)ph〉=1.396 (2)Å, r(C1–C7)=1.475 (12)Å, r(C8–Br)=1.884 (9)Å, ∠Br–C8C7=122 (2)°, ∠C1–C7C8=124 (2)°, ∠C7–C1–C2=123° (assumed value) and τ(C8C7–C1–C2)=40 (10)°.

Molecular structures and conformational compositions of 2-chlorobutane and 2-bromobutane; an investigation using gas-phase electron-diffraction data and ab initio molecular orbital calculations

The structure and conformational composition of 2-chlorobutane and 2-bromobutane have been studied by gas-phase electron diffraction (GED) at 25°C, together with ab initio molecular orbital calculations (HF/6-311+G(d,p)). These molecules may exist as three distinguishable conformers (G+, A, and G−). The symbols refer to anti (A) with a torsion angle Φ2(X8–C2–C3–C4) of about 180° and gauche (G+ and G−) with torsion angles Φ2(X8–C2–C3–C4) of about +60° and 300°(−60°), respectively. It was not possible; from our GED-data alone, to accurately determine the conformational composition because the distance distributions for two of the conformers (G+ and G−) are very similar. The conformational composition for 2-chlorobutane obtained from the ab initio calculations (G+ 62%, A 25% G− 13%) was found to fit the experimental data quite well. For 2-bromobutane the ab initio calculated conformational composition (G+ 58%, A 28% G− 14%) did not, however, fit the experimental data. Here a much better fit was obtained by using only 10% of the A conformer and using the relative energy for the two gauche conformers, as obtained in the ab initio molecular orbital calculations, to calculate the relative amounts of the two gauche forms (G+ 73%, A 10% G− 17%). The results for the principal distances (rg) and angles ∠α for the G+ conformer of 2-chlorobutane, with estimated 2σ uncertainties, obtained from the combined GED/ab initio study are: r(C1–C2)=1.524(3)Å,r(C2–C3)=1.528(3)Å,r(C3–C4)=1.539(3)Å,r(C–Cl)=1.812(3)Å,r(C–H)ave=1.098(4)Å, ∠C1C2C3=111.5(16)°, ∠C2C3C4=113.3(5)°, ∠C1C2C1=110.4(9)°. The results for the G+ conformer of 2-bromobutane are: r(C1–C2)=1.526(4)Å,r(C2–C3)=1.530(4)Å,r(C3–C4)=1.540(4)Å,r(C–Br)=1.982(5)Å,r(C–H)ave=1.111(8)Å, ∠C1C2C3=112.5(16)°, ∠C2C3C4=114.6(15)°, ∠C1C2Br=110.1(16)°. Only average values for r(C–C), r(C–H), ∠CCC, and ∠CCH could be determined in the least-squares refinements, the differences between these parameters in the same conformer, and between the different conformers, were kept constant at the values obtained in the ab initio molecular orbital calculations.

Molecular structure and conformation of peroxydisulfuryl difluoride, S2O6F2, as determined by gas-phase electron diffraction and ab initio molecular orbital calculations

The structure and conformational composition of peroxydisulfuryl difluoride, S2O6F2, have been investigated by gas-phase electron diffraction. Some of the results from ab initio molecular orbital calculations (MP2/6-311+G∗) were used as constraints in the analysis. There is both experimental and theoretical evidence that only conformers with a gauche X–O–O–X torsion angle are present in the gaseous sample. Of these, only two conformers of symmetry C2 (G+G+and G−G−) and one of symmetry C1 (G+G−), where G± designates positive/negative rotation around the O–S bonds at either end of the molecule) were found to be plausible components of the gaseous mixture. In experiments at 298K, about equally good fits were found with two models, model A consisting of a ratio of G−G−/G+G+ equal to 57/43 (2σ=27), and model B consisting of a ratio of G−G−/G+G− equal to 38/62 (2σ=14). The composition of model A corresponds to ΔG0=G0(G+G+)−G0(G−G−)=0.17(σ=0.24) kcal/mol, and that of model B to ΔG0=G0(G+G−)−G°(G−G−)=−0.29(σ=0.12). A system composed of only C2 symmetry conformers, such as model A, is favored by IR and Raman data, but our electron-diffraction results do not allow a choice. However, the bond lengths and bond angles for all conformers are similar so that, except for the torsion angles, the parameter values for the G−G− form are also reasonably close to those in the other forms. These distances (rg (Å)) and angles (∠α (°)) values with 2σ uncertainties are r(SO)=1.406(2) Å, r(S–F)=1.539(3) Å, r(O–S)=1.620(4) Å, r(O–O)=1.453(14) Å, 〈∠(O–SO)〉=1/2[(O–SO4)+∠(O–SO5)]=107.2(12)°, Δ∠(O–SO)=∠(O–SO4)−∠(O–SO5)=8.1° (assumed), ∠(O–S–F)=98.2(18)°, ∠(O–O–S)=108.6(10)°, ∠(OSO)=126.7(15)°, and ∠(S–O–O–S)=122.7(56)°.

Perfluoroalkanes: Conformational Analysis and Liquid-State Properties from ab Initio and Monte Carlo Calculations

Classical OPLS-AA force-field parameters are developed for perfluoroalkanes primarily by fitting to conformational profiles from gas-phase ab initio calculations (LMP2/cc-pVTZ(-f)//HF/6-31G*) and to experimental data for pure liquids. The ab initio C−C−C−C profile of n-C4F10 (perfluorobutane) is similar to those from prior high-level calculations and indicates the presence of gauche (g) and ortho (o) minima and of anti (a) minima slightly offset from 180°. Ab initio torsional profiles for n-C5F12 (perfluoropentane) and (CF3)2CFCF2CF3 (perfluoro-2-methylbutane) also show three sets of energy minima. Special OPLS-AA torsional parameters for these three molecules closely match ab initio and experimental geometries, conformational energies (ΔEmin), and conformational energy barriers. These specialized force fields were merged to provide a generalized force field for linear, branched, and cyclic perfluoroalkanes. The resultant parameters yield key ΔEmin values within 0.6 kcal/mol of the ab initio results for the three test compounds but more poorly represent the energy barriers. The parametrization also included reproduction of experimental liquid properties of these compounds, CF4 (perfluoromethane) and c-C5F10 (perfluorocyclopentane) via Monte Carlo (MC) simulations. MC simulations of six additional molecules were also performed in order to test the transferability of the force field.

Structural and conformational analysis of 1-monofluorosilacyclobutane and 1-monochlorosilacyclobutane. A gas-phase electron diffraction and ab initio investigation

The structures of numerous 1,1-disubstituted silacyclobutanes have been investigated thoroughly, but none of the monosubstituted representatives have been studied as yet. In the present work the geometric structures and conformational equilibria of 1-monofluorosilacyclobutane (MFSCB) and 1-monochlorosilacyclobutane (MCSCB) have been investigated by means of gas-phase electron diffraction and ab initio calculations. The conformational analysis reveals that both molecules are present with both equatorial and axial conformations. Consistent with one another, the electron diffraction data and the ab initio results show that the equatorial conformers of MFSCB and MCSCB are more stable than the higher energy axial forms. The experiments demonstrate that the equatorial conformers of MFSCB and MCSCB are lower in energy than the axial conformers by 4.30 (0.21)kJ/mol (corresponding to eq:ax=85:15 (5)) and 3.92 (0.23)kJ/mol, (eq:ax=83:17 (6)), respectively. For comparison, ab initio calculations at the MP/6-31G(d,p) level predict energy differences of 6.04 and 3.43kJ/mol, respectively, in favor of the equatorial forms of MFSCB and MCSCB. During the structural refinement it was assumed that all of the structural parameters except the puckering angle θ for both the equatorial and axial conformers are equal. This assumption was supported by the ab initio calculations. The major (ra) bond distances and bond angles which were obtained from the final refinement of the experimental data are (with uncertainties of 3σ) for MFSC: r(Si–C)=1.855(1)Å,r(Si–F)=1.592(2)Å,r(C–H)=1.089(3)Å, ∠(H–Si–F)=106.8(6)°, ∠(C–Si–C)=80.8(6)°, ∠(C–C–C)=98.6(19)° and the puckering angles θeq=37.4(20)° and θax=23.5(70)°. For MCSCB the following structural parameters were obtained: r(Si–C)=1.864(2)Å,r(Si–Cl)=2.059(3)Å,r(Si–H)=1.470(12)Å,r(C–C)=1.591(5)Å,r(C–H)=1.112(4)Å, ∠(H–Si–Cl)=106.0(6)°, ∠(C–Si–C)=80.7(14)°, ∠(C–C–C)=98.7(22)°. The puckering angles were found to be θeq=34.2(25)° and θax=21.5(50)°. The observed simultaneous reduction of the Si–C and the Si–F(Cl) bonds can be examined by electrostatic arguments and other concepts such as bond polarity, negative hyperconjugation and carbon(2pπ)–silicon(3pπ) orbital overlap.By applying various ab initio methods such as HF/6-31G(d,p), MP2/6-31G(d,p) and DFT/b3pw91/6-31G(p) the structures and conformations of mono- and dihalogenated silacyclobutanes of the type (CH2)3SiY (Y=HF, HCl, HBr, HI, H2, F2, Cl2, Br2 and I2) have been investigated. Our results show that there is a regular increase of the preferability of the equatorial conformer with the increase of the electronegativity of the halogen atom. This finding is consistent with the correlation which was postulated earlier by Jonvik and Boggs [4–7] for monosubstituted cyclobutanes. In order to gain more insight regarding the influence of the electronegativity of the substituent on the degree of strain in silacyclobutanes and for the purpose of comparison of the structures of different mono- and dihalogenated acyclic silanes and silacyclic compounds of larger size, as silacyclopentane and silacyclohexane have been also computed.

Gas-Phase Molecular Structure of 2-Halo-1,3-dihetero-2-phospholanes

The molecular structure of 2-chloro-1,3-dithia-2-phospholane was determined using gas-phase electron diffraction and ab initio calculations. The heteroring in the molecule has an asymmetric structure like a symmetric P-envelope twisted about the C-C bond with an axial P-Cl bond. Geometric parameters of the molecule and mean vibration amplitudes were determined. The molecular structure of 2-chloro-1,3-oxathia-2-phospholane was predicted. The molecule in the gas phase has two conformers [twisted C(O)- and C(S)-envelope] with an axial P-Cl bond.

Electronic spectra, excited-state geometries and molecular electrostatic potentials of aromatic amino acids

Lowest singlet excitation and emission energies of the three aromatic amino acids (phenylalanine, tyrosine and tryptophan) that are known to absorb ultraviolet radiation strongly were obtained using gas phase ab initio calculations. The 3-21G basis set was used and the excited states were generated using configuration interaction involving singly excited configurations (CIS). The calculated excitation and emission energies reproduce the observed trends satisfactorily. The changes in geometry consequent to excitation take place in the molecules mainly in the corresponding six-membered rings. The rings of phenylalanine and tyrosine get somewhat expanded consequent to excitation. This is in qualitative agreement with experimental results on substituted benzenes obtained from high resolution spectroscopy. The changes in the geometry of tryptophan following excitation are somewhat different from those of phenylalanine and tyrosine. Ground and excited state molecular electrostatic potentials suggest that hydrogen bonding patterns of the three amino acids would not change appreciably following electronic excitation of the molecules which explains why structures and activities of proteins and enzymes are not seriously modified on ultraviolet irradiation.

Sakurai addition and ring annulation of allylsilanes with alpha, beta-unsaturated esters. Experimental results and ab initio theoretical predictions examining allylsilane reactivity

Trimethylallylsilane has been shown to add to methyl acrylate in good yield when catalyzed by TiCl(4) at room-temperature despite literature reporting to the contrary. Further, even with these small alkyl ligands on the metal, ring annulation occurs to a large extent, in addition to simple allylation (Sakurai addition). The kinetic product is the ((trimethylsilyl)methyl)cyclobutane derivative which can be isomerized to cyclopentanoid, the thermodynamic product, if left in the presence of the catalyst. Consistent with other literature in this area, increasing the size of the ligands on silicon increases both the rate of product formation and the proportion of ring annulation relative to allylation. To develop a predictive model for allylsilane reactivity, ab initio gas-phase calculations have been made on the parent allylsilane with different ligands on the metal and on the reaction between these allylsilanes and acrolein, acrylic acid, and methyl acrylate. Predictions indicate that as the length of n-alkyl ligands on silicon increase, so does the apparent ability of the Si-Calpha bond of the allylsilane to hyperconjugate with developing vacant p orbital on Cbeta as the allylsilane begins to attack an electrophile. This is corroborated by a gradually increasing HOMO in the ground-state allylsilane as the ligands are changed from methyl through to n-hexyl and an increasing Si-Calpha bond length and decreasing Si-Calpha-Cbeta bond angle in the protonated species. These results in the gas phase mirror the reactivity of these n-alkyl-substituted allylsilanes in experiment; i.e., as the length of the alkyl chain increases, reactivity increases significantly. Triisopropylallylsilane, a very reactive silane, appears to anomalous in charge distribution and geometrical features compared with other substituted allylsilane systems which is due, presumably, to steric effects. The calculations on the protonated species would indicate that almost no hyperconjugative stabilization can occur on the basis of the bond lengths and angles necessary to promote good orbital overlap between the Si-Calpha bond and the empty p orbital on Cbeta. However, the gas-phase reaction of the triisopropylallylsilane with acrolein and methyl acrylate led to comparatively low energy barriers of 13.1 and 24.5, respectively, which is consistent with its high experimental reactivity. Together, this computational analysis has produced a useful model for predicting allylsilane reactivity and some possible explanations for this reactivity.

Molecular structure of tetramethoxygermane, Ge(OCH 3) 4, determined by gas-phase electron diffraction and ab initio molecular orbital calculations

The structure of tetramethoxygermane, Ge(OCH 3) 4, has been determined by gas-phase electron diffraction (GED) and ab initio molecular orbital calculations. Two distinct conformational geometries are feasible for this molecule, one having S 4 symmetry and the other D 2d symmetry. The S 4 conformer was calculated to be about 3 kcal mol −1 lower in energy than the D 2d conformer. Refinements, based upon a dynamic model with S 4 symmetry, gave a satisfactory fit to the experimental data. Results for the principal distances ( r g) and angles ∠ α from the combined GED/ab initio, with estimated 2 σ uncertainties are: r(Ge–O)=1.743(3), r(C–O)=1.413(5), r( C– H) ave =1.075(13) A ̊ ; ∠O 2GeO 7=110.1(19), ∠GeOC=122.7(8), ∠OCH ave=109.9(24), Φ(C 3O 2GeO 7)=72° (ab initio), Φ(H 6C 3O 2Ge)=176° (ab initio).

Conformational Composition of Gaseous trans-1,4-Dichlorocyclohexane. Molecular Structures and Energy Differences of the aa and ee Components from Gas-Phase Electron Diffraction and ab Initio Calculations

Electron-diffraction patterns from gaseous trans-1,4-dichlorocyclohexane at a temperature of 105 °C have been analyzed with the help of results from ab initio molecular orbital calculations to yield the structures of the ee and aa forms (equatorially and axially disposed chlorine atoms, respectively) of the molecule and the composition of the mixture. The model of this complicated system was defined in terms of the structure of the ee form, tying many of the parameters of the aa form to those of the ee by parameter differences calculated ab initio. Some of the results (rg/Å, ∠e/deg; 2σ uncertainties) for the ee (aa) forms from the preferred model are 〈r(C−H)〉 = 1.115(4) (1.113); r(C1−C2) = 1.525(6) (1.525); r(C2−C3) = 1.542(13) (1.535); r(C−Cl) = 1.799(3) (1.812); r(Cl···Cl) = 6.309(11) (5.236); ∠(C2C1C6) = 109.9(14) (110.1); ∠(CCCl) = 109.7(4) (109.8); flap (the angle between the planes C2C1C6 and C2C3C5C6) = 51.7(19) (47.2(12)). The mole fraction of the ee form was determined to be 0.46(6). The structural predictions of ab initio calculations were tested by optimizations at several levels, among them HF/6-31G*, MP2/6-311G*, QCISD/6-311+G(2df,p), MPw1PW91/6-311G*, B3P86/6-311G*, and B3P86/6-311+G(2df,p). Parameter values from each of these calculations are in good agreement with experiment, but those from the HF/6-31G* are poorest. The experimental composition is most accurately predicted by the MP2/6-311G* and QCISD/6-311+G(2df,p) calculations from the conformational energy differences ΔEtheor corrected for zero-point energy and entropy differences. The composition of the system is discussed in relation to that of monochlorocyclohexane.

A reinvestigation of the molecular structure of dimethyl-N-nitramine by gas electron diffraction, ab initio calculations of the molecular geometry and the force field and vibrational spectra

The molecular structure of dimethyl-N-nitramine was reinvestigated with gas-phase electron diffraction (ED) and ab initio calculations. Ab initio calculations using different basis sets and HF, MP2 and DFT all predict a molecule with Cs symmetry and a pyramidal amine N bond configuration. The vibrational spectra were interpreted from the scaling of the harmonic force field, and vibrational amplitudes required for the ED analysis were calculated from this scaled force field. The following values (rg bond lengths in Å and ∠α angles in degrees with errors equal to three standard deviations) were found for the main parameters: r(N–O)=1.232(3), r(N–N)=1.387(3), r(N–C)=1.466(3), r(C–H)ave=1.114(9), ∠CCN=116.1(6), ∠CNC=122.4(27), ∠ONO=127.6(12), ∠NCHave=109.9(18). The sum of the bond angles around the amine N atom is 354.6(28)°. The geometrical parameters obtained from the ED analysis are in agreement with the ab initio calculations except that a more pyramidal amine N bond configuration is predicted by ab initio.

OPLS All-Atom Model for Amines: Resolution of the Amine Hydration Problem

Classical force-field parameters have been developed for amines primarily by fitting to experimental data for pure liquids and to hydrogen-bond strengths from gas-phase ab initio calculations. The resultant parameters were used to calculate relative free energies of hydration for ammonia, methylamine, dimethylamine, and trimethylamine using free energy perturbation calculations in Monte Carlo simulations (MC/FEP). The results including the fact that the most favorable ΔGhyd occurs for methylamine are in excellent agreement with the experimental data, in contrast to numerous prior computational reports. The calculations reveal two opposing trends in water: increased contribution from hydrogen-bond acceptance and diminished contribution from hydrogen-bond donation with increasing methylation of the amines. The proper balance of hydrogen-bond strengths, which is achieved with the OPLS-AA force field, is essential for correct ordering of the free energies of hydration. MC simulations for the pure liquids of thirteen additional amines, not included in the original parametrization, then demonstrated the transferability of the force field. These simulations covered aliphatic as well as cyclic and aromatic amines. Furthermore, the appropriateness of the force field for less polar environments was confirmed through MC/FEP calculations of relative free energies of solvation and log P values in chloroform. It is apparent that the prior problems with classical force fields for amines were simply a result of nonoptimal parametrization rather than to a critical omission such as the lack of explicit polarization.

Computation of the Electronic and Spectroscopic Properties of Carbohydrates Using Novel Density Functional and Vibrational Self-Consistent Field Methods

ABSTRACT A novel density functional method is presented for the calculation of electronic and thermodynamical properties of oligosaccharides. This method, termed K2-BVWN, offers two advantages; it scales as N 3, where N is the number of basis functions, and there are only two adjustable parameters. The current density functional method is tested in terms of reproducing high level gas phase ab initio calculations in eleven low energy conformers of D-glucopyranose including exo-anomeric and different hydroxymethyl orientations (G −, G +, and T). The K2-BVWN method is also tested in terms of reproducing the spectroscopic features of D-glucopyranose and D-mannopyranose (α/β) as compared with both a vibrational self-consistent field calculation (VSCF) as well as experimental infrared spectroscopy. The VSCF calculations offer the advantage that it is possible to include higher order mode coupling and anharmonic effects directly into the calculation of the vibrational frequencies. In general, the K2-BVWN method reproduces the ab initio energetic trends of the different conformers of D-glucose. While the absolute energies are not the same between the ab initio and the K2-BVWN method, both methods do predict a preference for the α-anomer in the gas phase (0.4 kcal/mol ab initio, 0.0 – 0.5 kcal/mol K2-BVWN). The K2-BVWN method was able to reproduce the experimental and VSCF calculated spectrum of both D-glucopyranose and D-mannopyranose in the frequency range between 1500 – 800 cm−1. Because the current density functional method is both relatively quick and accurate, it represents a significant advancement in the development of oligosaccharide force fields.

Molecular Structure and Conformation of Dimethyltrisulfane, CH(3)SSSCH(3), As Determined by ab Initio Molecular Orbital Calculations and Gas-Phase Electron Diffraction.

Gas-phase electron diffraction and ab initio calculations suggest dimethyltrisulfane exist as a mixture of G+G+ (C2 symmetry) and G+G- (Cs symmetry) forms with the former lower in energy. The C−S−S−S dihedral angle for the G+G+ form is about 80°.

Molecular structure of phenylsilane: a study by gas-phase electron diffraction and ab initio molecular orbital calculations

The molecular structure of phenylsilane has been determined accurately by gas-phase electron diffraction and ab initio MO calculations at the MP2(f.c.)/6-31G* level. The calculations indicate that the perpendicular conformation of the molecule, with a Si–H bond in a plane orthogonal to the plane of the benzene ring, is the potential energy minimum. The coplanar conformation, with a Si–H bond in the plane of the ring, corresponds to a rotational transition state. However, the difference in energy is very small, 0.13 kJ mol −1, implying free rotation of the substituent at the temperature of the electron diffraction experiment (301 K). Important bond lengths from electron diffraction are: < r g(C–C)>=1.403±0.003 Å, r g(Si–C)=1.870±0.004 Å, and r g(Si–H)=1.497±0.007 Å. The calculations indicate that the C ipso –C ortho bonds are 0.010 Å longer than the other C–C bonds. The internal ring angle at the ipso position is 118.1±0.2° from electron diffraction and 118.0° from calculations. This confirms the more than 40-year old suggestion of a possible angular deformation of the ring in phenylsilane, in an early electron diffraction study by F.A. Keidel, S.H. Bauer, J. Chem. Phys. 25 (1956) 1218.

Hybrid ab Initio Quantum Mechanics/Molecular Mechanics Calculations of Free Energy Surfaces for Enzymatic Reactions: The Nucleophilic Attack in Subtilisin

An effective approach for ab initio calculations of activation free energies of enzymatic reactions is developed and examined. This approach uses an empirical valence bond (EVB) potential surface as a reference potential for evaluating the free energies of a hybrid ab initio quantum mechanics/molecular mechanics (QM(ai)/MM) potential surface. This procedure involves an automated calibration of the EVB potential using gas-phase ab initio calculations. In addition, strategies for treating the contact region of QM and MM atoms as well as enzyme and solvent environments are developed. Two levels of ab initio calculations are used in studying the QM atoms: the HF/4-31G method, which allows calculations on a large number of points while still giving accurate results, and the MP2/6-31+G* approach. The QM(ai)/MM method is implemented and examined by simulating the nucleophilic attack step in the catalytic reaction of subtilisin. It is found that the use of the EVB potential as a reference allows one to obtain th...

Separation of Ground State and Transition State Effects in Intramolecular and Enzymatic Reactions. 2. A Theoretical Study of the Formation of Transition States in Cyclic Anhydride Formation

Ab initio gas phase calculations at the RHF/6-31+G(d) level have been used to define the geometries of the transition states for the intramolecular displacement reactions with monophenyl esters of glutaric (I), succinic (II), and 3,6-endoxo-Δ4-tetrahydrophthalic (III) acids to provide the corresponding anhydrides plus phenolate. As determined experimentally, the rate determining step was found to involve transition states in which phenoxide is departing. Intrinsic reaction coordinate (IRC) calculations from transition state toward reactant and product sides provided intramolecular ion−molecule complexes (IIMC) of I and II and the tetrahedral intermediate of III and the product ion−molecule complexes (IMC) of the phenoxide and anhydride of I, II, and III. Vibrational frequency calculations were performed for all stationary states. Single point calculations using an electron correlation method and different solvation methods were performed on optimized reactant side gas phase geometries. The transition states formed from I, II, and III are essentially identical in bond lengths (ester carbon to leaving phenoxide 1.77, 1.79, or 1.80 Å; carbonyl oxygen to ester carbon 1.20 or 1.21 Å; nucleophilic oxygen to ester carbon 1.44 or 1.43 Å; and α-carbon to ester carbon 1.52 or 1.53 Å) and angles (characterized by the attacking oxygen, ester carbon, and leaving oxygen 97.8°, 97.3°, 96.7°; attacking oxygen, ester carbon, and ester carbonyl oxygen 117.0°, 117.4°, 113.7°). Transition state stabilization as a result of restricting low frequency vibrations is determined by comparing the frequencies of the IIMC (and tetrahedral intermediate) to the corresponding TS. The total number of frequencies does not change in going from the IIMC (or TI) to the TS for each ester. For those frequencies lower than 1000 cm-1, the number of frequencies remains constant. On comparing the ratio between the number of frequencies below 1000 cm-1 and the total number of frequencies in the transition states formed from I, II, and III, we find 0.49, 0.51, and 0.55, respectively. By the criteria of superimposable TS structures and lack of evidence for frequency changes in the TS in the direction of increasing rate, we conclude that the rate ratios of ∼230-fold in comparing I/II and II/III reside in ground state phenomena. This conclusion is supported by the geometries of IIMC and TS structures. Gas phase reaction coordinates and derived enthalpy and entropy values are provided and discussed. Conversion of ground state intramolecular anion ester complexes (IIMC) of esters I and II to their respective TSs involves a decrease in computed ΔH⧧ while ΔS⧧ remains invariant. In a previous investigation, the formation of ground state conformations (NACs) of geometry that allows entrance to the IIMC and then TS was found to be related to ΔH° rather than ΔS°. The importance of these findings to a general concept of entropy driven kinetic processes is discussed.