Combination of molecular dynamics method and 3D-RISM theory for conformational sampling of large flexible molecules in solution

We have developed an algorithm for sampling the conformational space of large flexible molecules in solution, which combines the molecular dynamics (MD) method and the three-dimensional reference interaction site model (3D-RISM) theory. The solvent-induced force acting on solute atoms was evaluated as the gradient of the solvation free energy with respect to the solute-atom coordinates. To enhance the computation speed, we have applied a multiple timestep algorithm based on the RESPA (Reversible System Propagator Algorithm) to the combined MD/3D-RISM method. By virtue of the algorithm, one can choose a longer timestep for renewing the solvent-induced force compared with that of the conformational update. To illustrate the present MD/3D-RISM simulation, we applied the method to a model of acetylacetone in aqueous solution. The multiple timestep algorithm succeeded in enhancing the computation speed by 3.4 times for this model case. Acetylacetone possesses an intramolecular hydrogen-bonding capability between the hydroxyl group and the carbonyl oxygen atom, and the molecule is significantly stabilized due to this hydrogen bond, especially in gas phase. The intramolecular hydrogen bond was kept intact during almost entire course of the MD simulation in gas phase, while in the aqueous solutions the bond is disrupted in a significant number of conformations. This result qualitatively agrees with the behavior on a free energy barrier lying upon the process for rotating a torsional degree of freedom of the hydroxyl group, where it is significantly reduced in aqueous solution by a cancellation between the electrostatic interaction and the solvation free energy.     

Prediction of cyclohexane-water distribution coefficient for SAMPL5 drug-like compounds with the QMPFF3 and ARROW polarizable force fields

We present the performance of blind predictions of water—cyclohexane distribution coefficients for 53 drug-like compounds in the SAMPL5 challenge by three methods currently in use within our group. Two of them utilize QMPFF3 and ARROW, polarizable force-fields of varying complexity, and the third uses the General Amber Force-Field (GAFF). The polarizable FF’s are implemented in an in-house MD package, Arbalest. We find that when we had time to parametrize the functional groups with care (batch 0), the polarizable force-fields outperformed the non-polarizable one. Conversely, on the full set of 53 compounds, GAFF performed better than both QMPFF3 and ARROW. We also describe the torsion-restrain method we used to improve sampling of molecular conformational space and thus the overall accuracy of prediction. The SAMPL5 challenge highlighted several drawbacks of our force-fields, such as our significant systematic over-estimation of hydrophobic interactions, specifically for alkanes and aromatic rings.     

Dependence of chymosin and pepsin partition coefficient with phase volume and polymer pausidispersity in polyethyleneglycol-phosphate aqueous two-phase system

The influence of the phase volume ratio and polymer pausidispersity on chymosin and pepsin partition in polyethylenglycol-phosphate aqueous two-phase systems was studied. Both proteins showed a high affinity for the polyethylenglycol rich phase with a partition coefficient from 20 to 100 for chymosin and from 20 to 180 for pepsin, when the polyethyleneglycol molecular mass in the system varied between 1450 and 8000. The partition coefficient of chymosin was not affected by the volume phase ratio, while the pepsin coefficient showed a significant decrease in its partition coefficient with the increase in the top/bottom phase volume ratio.     

Assessment of density functionals with long‐range and/or empirical dispersion corrections for conformational energy calculations of peptides

Density functionals with long‐range and/or empirical dispersion corrections, including LC‐ωPBE, B97‐D, ωB97X‐D, M06‐2X, B2PLYP‐D, and mPW2PLYP‐D functionals, are assessed for their ability to describe the conformational preferences of Ac‐Ala‐NHMe (the alanine dipeptide) and Ac‐Pro‐NHMe (the proline dipeptide) in the gas phase and in water, which have been used as prototypes for amino acid residues of peptides. For both dipeptides, the mean absolute deviation (MAD) is estimated to be 0.22–0.40 kcal/mol in conformational energy and 2.0–3.2° in torsion angles ? and ψ using these functionals with the 6‐311++G(d,p) basis set against the reference values calculated at the MP2/aug‐cc‐pVTZ//MP2/aug‐cc‐pVDZ level of theory in the gas phase. The overall performance is obtained in the order B2PLYP‐D ≈ mPW2PLYP‐D > ωB97X‐D ≈ M06‐2X > MP2 > LC‐ωPBE > B3LYP with the 6–311++G(d,p) basis set. The SMD model at the M06‐2X/6‐31+G(d) level of theory well reproduced experimental hydration free energies of the model compounds for backbone and side chains of peptides with MADs of 0.47 and 4.3 kcal/mol for 20 neutral and 5 charged molecules, respectively. The B2PLYP‐D/6‐311++G(d,p)//SMD M06‐2X/6‐31+G(d) level of theory provides the populations of backbone and/or prolyl peptide bond for the alanine and proline dipeptides in water that are consistent with the observed values. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Adiabatic and non-adiabatic corrections to rovibrational energies of diatomic molecules: variational calculations with experimental accuracy

Using the variational technique, eigensolutions of the radial Herman-Asgharian equation accounting for non-adiabatic terms are determined within the experimental accuracy of the high-resolution spectroscopy. This method, which is independent of the algebraic and numerical approaches currently used in the literature for a "direct-potential-fit" of diatomic rovibrational spectra, is shown to be useful for validation of available calculations and for resolving some controversial issues. Comparative discussions are reported in this paper for a dozen diatomic molecules.     

Standard partial molar volumes of aqueous glycolic acid and tartaric acid from 25 to 350 degrees C: evidence of a negative Krichevskii parameter for a neutral organic solute

Apparent molar volumes have been determined using a high-pressure vibrating-tube densimeter for aqueous solutions of glycolic acid (HGly = HOCH(2)COOH) and tartaric acid (H(2)Tar = HOOCCH(OH)CH(OH)COOH) at temperatures from 25 degrees C to 350 degrees C and pressures as high as 20 MPa. The resulting standard partial molar volumes (HGly,aq) are relatively independent of temperature until 315 degrees C, at which point (HGly,aq) deviates sharply toward negative values. This suggests that the Krichevskii parameter, A(Kr) = lim(x(2) --> 0) , which describes the discontinuities in standard partial molar properties at the critical point of water, is negative. Almost all aqueous nonelectrolytes are characterized by positive Krichevskii parameters. This is the first negative value reported for any organic molecule that is not an ion or zwitterion and only the third ever observed directly for a neutral species (the others are B(OH)(3) and H(3)PO(4)). The standard partial molar volumes for H(2)Tar(aq) are also relatively independent of temperature until 275 degrees C, suggesting a similar behavior. However, the onset of thermal decomposition prevented measurements at temperatures above 300 degrees C.     

Unexpected conformational properties of 1-trifluoromethyl-1-silacyclohexane, C5H10SiHCF3: gas electron diffraction, low-temperature NMR spectropic studies, and quantum chemical calculations

The molecular structure of axial and equatorial conformers of 1-trifluoromethyl-1-silacyclohexane, (C5H10SiHCF3), as well as the thermodynamic equilibrium between these species was investigated by means of gas electron diffraction (GED), dynamic nuclear magnetic resonance (DNMR) spectroscopy, and quantum chemical calculations (B3LYP, MP2, and CBS-QB3). According to GED, the compound exists as a mixture of two Cs symmetry conformers possessing the chair conformation of the six-membered ring and differing in the axial or equatorial position of the CF3 group (axial=58(12) mol%/equatorial=42(12) mol%) at T=293 K. This result is in a good agreement with the theoretical prediction. This is, however, in sharp contrast to the conformational properties of the cyclohexane analogue. The main structural feature for both conformers is the unusually long exocyclic bond length Si--C 1.934(10) A. A low-temperature 19F NMR experiment results in an axial/equatorial ratio of 17(2) mol%:83(2) mol% at 113 K and a DeltaG (not equal) of 5.5(2) kcal mol-1. CBS-QB3 calculations in the gas-phase and solvation effect calculations using the PCM(B3LYP/6-311G*) and IPCM(B3LYP/6-311G*) models were applied to estimate the axial/equatorial ratio in the 100-300 K temperature range, which showed excellent agreement with the experimental results. The minimum energy pathways for the chair-to-chair inversion of trifluoromethylsilacyclohexane and methylsilacyclohexane were also calculated using the STQN(Path) method.     

System with variable energy,volume and number of particles: Evaluation of partition function and thermodynamic quantities

Partition function and thermodynamic parameters of the system open with respect to energy E, volume V and number of particles N, whereas temperature T, chemical potential μ and pressure P were kept constant, were considered by the procedure proposed by Gibbs. The mean values of variable energy, volume and number of particles were obtained by universal expression for such values. The entropy was determined by its general statistical definition. The thermodynamic potential and other thermodynamic quantities were also turned out naturally.     

Improved description of the structure of molecular and layered crystals: ab initio DFT calculations with van der Waals corrections

The implementation of technique for full structural optimizations of complex periodic systems in the DFT-PAW package VASP, including the volume and shape of the unit cell and the internal coordinates of the atoms, together with a correction that allows an appropriate modeling of London dispersion forces, as given by the DFT-D2 approach of Grimme [Grimme, S. J. Comp. Chem. 2006, 27, 1787], is reported. Dispersion corrections are calculated not only for the forces acting on the atoms, but also for the stresses on the unit cell. This permits a simultaneous optimization of all degrees of freedom. Benchmark results on a series of prototype systems are presented and compared to results obtained by other methods and experimental data. It is demonstrated that the computationally inexpensive DFT-D2 scheme yields reasonable predictions for the structure, bulk moduli, and cohesive energies of weakly bonded materials.     

Vibrational assignments, normal coordinate analysis, B3LYP calculations and conformational analysis of methyl-5-amino-4-cyano-3-(methylthio)-1H-pyrazole-1-carbodithioate

The Raman and infrared spectra of solid methyl-5-amino-4-cyano-3-(methylthio)-1H-pyrazole-1-carbodithioate (MAMPC, C7H8N4S3) were measured in the spectral range of 3700-100 cm(-1) and 4000-200 cm(-1) with a resolution of 4 and 0.5 cm(-1), respectively. Room temperature 13C NMR and (1)H NMR spectra from room temperature down to -60 °C were also recorded. As a result of internal rotation around C-N and/or C-S bonds, eighteen rotational isomers are suggested for the MAMPC molecule (Cs symmetry). DFT/B3LYP and MP2 calculations were carried out up to 6-311++G(d,p) basis sets to include polarization and diffusion functions. The results favor conformer 1 in the solid (experimentally) and gaseous (theoretically) phases. For conformer 1, the two -CH3 groups are directed towards the nitrogen atoms (pyrazole ring) and CS, while the -NH2 group retains sp2 hybridization and C-CN bond is quasi linear. To support NMR spectral assignments, chemical shifts (δ) were predicted at the B3LYP/6-311+G(2d,p) level using the method of Gauge-Invariant Atomic Orbital (GIAO) method. Moreover, the solvent effect was included via the Polarizable Continuum Model (PCM). Additionally, both infrared and Raman spectra were predicted using B3LYP/6-31G(d) calculations. The recorded vibrational, 1H and 13C NMR spectral data favors conformer 1 in both the solid phase and in solution. Aided by normal coordinate analysis and potential energy distributions, confident vibrational assignments for observed bands have been proposed. Moreover, the CH3 barriers to internal rotations were investigated. The results are discussed herein are compared with similar molecules whenever appropriate.     

Evidence of conformational equilibrium of 1-ethyl-3-methylimidazolium in its ionic liquid salts: Raman spectroscopic study and quantum chemical calculations

Raman spectra of liquid 1-ethyl-3-methylimidazolium (EMI+) salts, EMI(+)BF4-, EMI(+)PF6-, EMI(+)CF3SO3-, and EMI(+)N(CF3SO2)2-, were measured over the frequency range 200-1600 cm(-1). In the range 200-500 cm(-1), we found five bands originating from the EMI+ ion at 241, 297, 387, 430, and 448 cm(-1). However, the 448 cm(-1) band could hardly be reproduced by theoretical calculations in terms of a given EMI+ conformer, implying that the band originates from another conformer. This is expected because the EMI+ involves an ethyl group bound to the N atom of the imidazolium ring, and the ethyl group can rotate along the C-N bond to yield conformers. The torsion energy for the rotation was then theoretically calculated. Two local minima with an energy difference of ca. 2 kJ mol(-1) were found, suggesting that two conformers are present in equilibrium. Full geometry optimizations followed by normal frequency analyses indicate that the two conformers are those with planar and nonplanar ethyl groups against the imidazolium ring plane, and the nonplanar conformer is favorable. It elucidates that bands at 241, 297, 387, and 430 cm(-1) mainly originate from the nonplanar conformer, whereas the 448 cm(-1) band does originate from the planar conformer. Indeed, the enthalpy for conformational change from nonplanar to planar EMI+ experimentally obtained by analyzing band intensities of the conformers at varying temperatures is practically the same as that evaluated by theoretical calculations. We thus conclude that the EMI+ ion exists as either a nonplanar or planar conformer in equilibrium in its liquid salts.     

Blind prediction of distribution in the SAMPL5 challenge with QM based protomer and p<Emphasis Type="Italic">K</Emphasis><Subscript>a</Subscript> corrections

The computation of distribution coefficients between polar and apolar phases requires both an accurate characterization of transfer free energies between phases and proper accounting of ionization and protomerization. We present a protocol for accurately predicting partition coefficients between two immiscible phases, and then apply it to 53 drug-like molecules in the SAMPL5 blind prediction challenge. Our results combine implicit solvent QM calculations with classical MD simulations using the non-Boltzmann Bennett free energy estimator. The OLYP/DZP/SMD method yields predictions that have a small deviation from experiment (RMSD = 2.3 \(\log\) D units), relative to other participants in the challenge. Our free energy corrections based on QM protomer and \({\text{p}}K_{\text{a}}\) calculations increase the correlation between predicted and experimental distribution coefficients, for all methods used. Unfortunately, these corrections are overly hydrophilic, and fail to account for additional effects such as aggregation, water dragging and the presence of polar impurities in the apolar phase. We show that, although expensive, QM-NBB free energy calculations offer an accurate and robust method that is superior to standard MM and QM techniques alone.     

Al3+ induced planarization, conformational arrest and metallochromic shift in a pyrimidine dione dye: insight from integrated hybrid quantum-classical calculations

In order to explore the possibilities of simulating metallochromism by modern molecular modeling, we apply a sequential hybrid quantum-classical approach to a prototype metallochromic system-the Al(3+) ion and pyrimidinedione (PY) dye complex. The complex shows several structural features with relevance for the metallochromism: the PY dye exhibits conformers with dynamical transitions between twisted structures, which are inhibited by the addition of the metal ion leading to planarization and a conformational arrest: the Al(3+) ion behaves like a structure-modifier for both intra and intermolecular degrees of freedom and with respect to the intermolecular solvation shell structure. The sequential approach that we have employed uses DFT/MM molecular dynamics for structure modeling and TDDFT/PCM for property modeling. The computed metallochromic shift between PY and the Al(PY)(3+) complex in DMSO solvent is obtained in excellent agreement with experiment. The results infer optimism for future use of such modeling techniques to design metallochromic indicators.     

Theoretical calculations of the chemical shifts of cyclo[n]phosphazenes for n = 2, 3, 4 and 5 (X2PN)n with X = CH3, F,Cl and Br: the effect of relativistic corrections

Abstract

Di, tri, tetra and pentacyclophosphazenes substituted on the phosphorus atoms by CH₃, F, Cl and Br atoms corresponding to (X₂PN)_n structures have been studied theoretically at the B3LYP/6-311++G(d,p) level. After a brief discussion of their geometries comparing them to those of the conjugated carbocycles, (CH)_n, of the same size, the absolute shieldings calculated with the GIAO and ZORA approximations will be reported. For the Cl and mainly for the Br substituted cyclo[n]-phosphazenes, relativistic corrections are absolutely necessary for ³¹P and useful for ¹⁵N chemical shifts.     

Numerical sensitivity of trajectories across conformational energy hypersurfaces from geometry optimized molecular orbital calculations: AM1, MNDO,and MINDO/3

The monocyclic β-lactam [[4(S)-methyl-2-oxo-1-azetidinyl]thia]acetic acid was studied by the semiempirical molecular orbital methods AM1, MNDO, and MINDO/3. Using the reaction coordinate option in the program MOPAC on VAX and Cray X-MP computers, the potential energy curve was calculated for rotation of the C2-N1-S-C torsional angle in the conformationally flexible side chain while optimizing all other geometrical variables in the molecule. The trajectory taken during geometry optimization was found to be sensitive to the computer, the program version, the convergence criteria, and the degree of code optimization used in the calculation. In order to reduce the likelihood of spurious results, conformational or reaction energy hypersurfaces need to be calculated with the more precise SCF convergence and minimization criteria available in programs for MINDO/3, MNDO, and AM1 calculations. The nitrogen in the model β-lactam antibiotic is predicted to invert periodically as the dihedral angle to the exocyclic N-substituent sweeps through 360°.     

Identification of the phase of a fluid using partial derivatives of pressure, volume, and temperature without reference to saturation properties: Applications in phase equilibria calculations

The phase of a fluid (liquid, vapor) at a given state is normally identified by comparing the properties of the fluid at the given state with saturation properties. In this paper we present a thermodynamic method for determining the phase of a fluid from the partial derivatives of pressure, volume and temperature without reference to saturated properties. The method has immediate application in a variety of phase equilibria calculations, particularly for liquid-liquid or vapor-liquid-liquid equilibria calculations in process simulators.     

Molecular orbital calculations on η3- and η5-hexadienyl complexes of the platinum metals; an analysis of their conformational preferences and fluxional characteristics

Extended Hückel molecular orbital calculations are reported for the η³- and η⁵-platinum metal complexes [Pt(η³-C₆H₇)(PH₃)₂]⁺ and [Pt(η⁵-C₆H₇)(PH₃)₂]⁺. The η³-geometry is found to be only 0.56 eV more stable than the η⁵-geometry. This leads to a low energy fluxional process in these molecules. The stereochemistry of this fluxional process is rationalised in terms of the conformational preferences of the [Pt(η⁵-C₆H₇)(PH₃)₂]⁺ ions.     

Gas‐phase reaction of Cl with dimethyl sulfide: Temperature and oxygen partial pressure dependence of the rate coefficient

The kinetics of the reaction of Cl atoms with dimethyl sulfide has been investigated using a relative rate technique. Experiments were performed with oxygen partial pressures of 0, 200, and 500 mbar at a total pressure of 1000 mbar (N₂ + O₂) over the temperature range 283–308 K in a 1080 L reactor using long path in situ Fourier transform infrared absorption spectroscopy to monitor the reactants. The 254 nm photolysis of trichloroacetyl chloride was used as the Cl atom source. Three reference hydrocarbons, cyclohexane, n‐butane, and propene were employed. Good agreement was found between the rate coefficients determined using the different reference compounds. The rate coefficients were found to decrease with increasing temperature at constant O₂ pressure and increase moderately with increasing O₂ partial pressure at constant temperature. The temperature dependences of the Cl atom reaction with dimethyl sulfide for the three O₂ partial pressure investigated can be expressed by the simple Arrhenius expressions: k = (4.22 ± 1.78) × 10^?13 exp((1968 ± 379)/T), k = (5.42 ± 1.85) × 10^?13 exp((1946 ± 381)/T), and k = (6.90 ± 2.04) × 10^?13 exp((1912 ± 381)/T). The errors are a combination of the 2σ statistical errors from the kinetic data analysis plus an estimated systematic error that includes the error in the reference hydrocarbon. The mechanistic implications of the results are discussed. © 2004 Wiley Periodicals, Inc. Int J Chem Kinet 37: 66–73, 2005     

Ester derivatives of hexahomotrioxacalix[3]naphthalenes: conformational and binding properties with alkali metal cations

The syntheses of the triesters formed between ethyl bromoacetate and hexahomotrioxacalix[3]naphthalene 8, and its tert-butyl analogue 11, are described. Depending on the conditions employed, cone or partial cone conformers are produced. The conformations appear to have some influence on their complexation in neutral medium, with alkali metal cations. The X-ray structure of the partial cone triester 10 is presented.