Macroscopic order and electro-optic response of dipolar chromophore-polymer materials.

This Minireview considers the key factors that govern the organization of macroscopic polarization in nonlinear optical systems obtained by electric poling of organic dipolar chromophores dissolved in polymer matrices. The macroscopic electric polarization depends on the thermodynamic state of the dipole system. The dependence of the paraelectric and antiferroelectric states of dipolar chromophores on the chromophore concentration and the strength of the poling field is discussed. Phase transitions between the para- and antiferroelectric states are investigated within the limits of the Ising and isotropic models for the chromophore dipoles and are considered for varying chromophore concentration, poling field strength, and macroscopic shape of the sample used for poling. The macroscopic polarization and electro-optic coefficient of the material change drastically upon phase transition. The theories are compared with the experimental data on the electro-optic coefficient dependence on the chromophore concentration. The isotropic dipole model shows excellent agreement with experiment for the chromophore systems most commonly used in nonlinear optics.     

Polarizable Atomic Multipole-based Molecular Mechanics for Organic Molecules

An empirical potential based on permanent atomic multipoles and atomic induced dipoles is reported for alkanes, alcohols, amines, sulfides, aldehydes, carboxylic acids, amides, aromatics and other small organic molecules. Permanent atomic multipole moments through quadrupole moments have been derived from gas phase ab initio molecular orbital calculations. The van der Waals parameters are obtained by fitting to gas phase homodimer QM energies and structures, as well as experimental densities and heats of vaporization of neat liquids. As a validation, the hydrogen bonding energies and structures of gas phase heterodimers with water are evaluated using the resulting potential. For 32 homo- and heterodimers, the association energy agrees with ab initio results to within 0.4 kcal/mol. The RMS deviation of hydrogen bond distance from QM optimized geometry is less than 0.06 ?. In addition, liquid self-diffusion and static dielectric constants computed from molecular dynamics simulation are consistent with experimental values. The force field is also used to compute the solvation free energy of 27 compounds not included in the parameterization process, with a RMS error of 0.69 kcal/mol. The results obtained in this study suggest the AMOEBA force field performs well across different environments and phases. The key algorithms involved in the electrostatic model and a protocol for developing parameters are detailed to facilitate extension to additional molecular systems.     

Prediction of SAMPL3 host-guest affinities with the binding energy distribution analysis method (BEDAM)

BEDAM calculations are described to predict the free energies of binding of a series of anaesthetic drugs to a recently characterized acyclic cucurbituril host. The modeling predictions, conducted as part of the SAMPL3 host-guest affinity blind challenge, are generally in good quantitative agreement with the experimental measurements. The correlation coefficient between computed and measured binding free energies is 70% with high statistical significance. Multiple conformational stereoisomers and protonation states of the guests have been considered. Better agreement is obtained with high statistical confidence under acidic modeling conditions. It is shown that this level of quantitative agreement could have not been reached without taking into account reorganization energy and configurational entropy effects. Extensive conformational variability of the host, the guests and their complexes is observed in the simulations, affecting binding free energy estimates and structural predictions. A conformational reservoir technique is introduced as part of the parallel Hamiltonian replica exchange molecular dynamics BEDAM protocol to fully capture conformational variability. It is shown that these advanced computational strategies lead to converged free energy estimates for these systems, offering the prospect of utilizing host-guest binding free energy data for force field validation and development.     

Chemical shift driven geometry optimization

A new method for refinement of 3D molecular structures by geometry optimization is presented. Prerequisites are a force field and a very fast procedure for the calculation of chemical shifts in every step of optimization. To the energy, provided by the force field (COSMOS force field), a pseudoenergy, depending on the difference between experimental and calculated chemical shifts, is added. In addition to the energy gradients, pseudoforces are computed. This requires the derivatives of the chemical shifts with respect to the coordinates. The pseudoforces are analytically derived from the integral expressions of the bond polarization theory. Single chemical shift values attributed to corresponding atoms are considered for structural correction. As a first example, this method is applied for proton position refinement of the D-mannitol X-ray structure. A crystal structure refinement with 13C chemical shift pseudoforces is carried out.     

Rotational spectra of 1-chloro-2-fluoroethylene. II. Equilibrium structures of the cis and trans isomer

Equilibrium structures for the cis and trans isomer of 1-chloro-2-fluoroethylene are reported. The structures are obtained within a least-squares fit procedure using the available experimental ground-state rotational constants for various isotopic species of both forms. Vibrational effects were eliminated before the analysis using vibration-rotation interaction constants derived from computed quadratic and cubic force fields with the required quantum chemical calculations carried out using second-order Moller-Plesset perturbation as well as coupled-cluster (CC) theory. The semiexperimental or empirical equilibrium geometries obtained in this way agree well with the corresponding theoretical predictions obtained from CC calculations [at the CCSD(T) level] after extrapolation to the complete basis-set limit and inclusion of core-valence correlation corrections. The present results allow a detailed analysis of the geometrical differences between the two forms of 1-chloro-2-fluoroethylene. They are also compared to the structural data available for other halogenated ethylenes.     

Absolute intensities of Raman trace scattering from bicyclo-[1.1.1]-pentane

Our previous theoretical studies have identified the Raman intensity parameter for the bridgehead C-H stretch in bicyclo-[1.1.1]-pentane as the largest for any saturated hydrocarbon yet considered, while the methylene C-H parameter is predicted to be ordinary. Theoretical methods including self-consistent field, static and time dependent density functional theory, and coupled cluster, all predict a large bridgehead intensity parameter, but differ widely in the actual value. We have synthesized bicyclo-[1.1.1]-pentane and recorded the absolute intensity Raman trace scattering spectra. The recorded intensity of a resonance polyad in the C-H stretching region has been resolved and distributed onto the fundamental modes through an anharmonic resonance analysis from a computed quartic force field. The experimental internal coordinate intensity parameters have been obtained and compared with those computed. Although the static and dynamic density functional values overestimate the parameter by 10%-18%, the values predicted at the coupled-cluster level are found to be correct to within experimental error.     

A potential with low point charges for pure siliceous zeolites

A modified CHARMM force‐field (ZHB potential) with low point charges for silica was previously proposed by Zimmerman et al. (J. Chem. Theory Comput. 2011, 7, 1695). The ZHB potential is advantageous for quantum mechanics/molecular mechanics simulations as it minimizes the electron spill‐out problems. In the same spirit, here we propose a modified ZHB potential (MZHB) by reformulating its bonding potential, while retaining the nonbonding potential as in the ZHB force‐field. We show that several structural and dynamic properties of silica, like the IR spectrum, distribution functions, mechanical properties, and negative thermal expansion computed using the MZHB potential agree well with experimental data. Further, transferability of MZHB is also tested for reproducing the crystallographic structures of several polymorphs of silica. © 2015 Wiley Periodicals, Inc.     

Alcohols,ethers, carbohydrates,and related compounds. I. The MM4 force field for simple compounds

Simple alcohols and ethers have been studied with the MM4 force field. The structures of 13 molecules have been well fit using the MM4 force field. Moments of inertia have been fit with rms percentage errors as indicated: 18 moments for ethers, 0.28%; 21 moments for alcohols, 0.22%. Rotational barriers and conformational equilibria have also been examined, and the experimental and ab initio results are reproduced substantially better with MM4 than they were with MM3. Much of the improvement comes from the use of additional interaction terms in the force constant matrix, of which the torsion-bend and torsion-torsion are particularly important. Induced dipoles are included in the calculation, and dipole moments are reasonably well fit. It has been possible for the first time to fit conformational energetic data for both open chain and cyclic alcohols (e.g., propanol and cyclohexanol) with the same parameter set. For vibrational spectra, over a total of 82 frequencies, the rms error is 27 cm(-1), as opposed to 38 cm(-1) with MM3. Both the alpha and beta bond shortening resulting from the presence of the electronegative oxygen atom in the molecule are well reproduced. The electronegativity of the oxygen is sufficient that one must also include not only the alpha and beta electronegativity effects on bond lengths, but also on angle distortions, if structures are to be well reproduced. The heats of formation of 32 alcohols and ethers were fit overall to within experimental error (weighted standard deviation error 0.26 kcal/mol).     

Parametrization of semiempirical models against ab initio crystal data: evaluation of lattice energies of nitrate salts

A method to estimate the lattice energies E(latt) of nitrate salts is put forward. First, E(latt) is approximated by its electrostatic component E(elec). Then, E(elec) is correlated with Mulliken atomic charges calculated on the species that make up the crystal, using a simple equation involving two empirical parameters. The latter are fitted against point charge estimates of E(elec) computed on available X-ray structures of nitrate crystals. The correlation thus obtained yields lattice energies within 0.5 kJ/g from point charge values. A further assessment of the method against experimental data suggests that the main source of error arises from the point charge approximation.     

Molecular mechanics. The MM3 force field for alkenes

The MM3 force field has been extended to include alkenes. Forty-five compounds were examined, and structures, conformational equilibria, heats of formation, and rotational barriers, were calculated. For a smaller representative group, the vibrational spectra and entropies were also calculated. In general, these quantities, except for the vibrational spectra, agree with available data to approximately within experimental error. The vibrational frequencies for a set of eight well-assigned structures were calculated to a root-mean-square error of 47 cm^?1.     

Force field parameters for the simulation of modified histone tails

We describe the development of force field parameters for methylated lysines and arginines, and acetylated lysine for the CHARMM all‐atom force field. We also describe a CHARMM united‐atom force field for modified sidechains suitable for use with fragment‐based docking methods. The development of these parameters is based on results of ab initio quantum mechanics calculations of model compounds with subsequent refinement and validation by molecular mechanics and molecular dynamics simulations. The united‐atom parameters are tested by fragment docking to target proteins using the MCSS procedure. The all‐atom force field is validated by molecular dynamics simulations of multiple experimental structures. In both sets of calculations, the computational predictions using the force field were compared to the corresponding experimental structures. We show that the parameters yield an accurate reproduction of experimental structures. Together with the existing CHARMM force field, these parameters will enable the general modeling of post‐translational modifications of histone tails. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Computer simulation of solid and liquid benzene with an atomistic interaction potential derived from ab initio calculations

Molecular dynamics atomistic simulations of solid and liquid benzene have been performed, employing a model intermolecular potential derived from quantum mechanical calculations. The ab initio database includes approximately 200 geometries of the benzene dimer with interaction energies computed at the MP2 level of theory. The accuracy of the modeled force field results is satisfactory. The thermodynamic and structural properties, calculated in the condensed phases, are compared with experimental data and previous simulation results. Single particle and collective dynamical properties are also investigated through the calculation of translational and rotational diffusion coefficients, reorientational dynamics, and viscosities. The agreement of these data with experimental measurements confirms the reliability of the proposed force field.     

Structural and Vibrational Characterization of the Chromophore Binding Site of Bacterial Phytochrome Agp1

Agp1 is a prototypical bacterial phytochrome from Agrobacterium fabrum harboring a biliverdin cofactor which reversibly photoconverts between a red‐light‐absorbing (Pr) and a far‐red‐light‐absorbing (Pfr) states. The reaction mechanism involves the isomerization of the bilin‐chromophore followed by large structural changes of the protein matrix that are coupled to protonation dynamics at the chromophore binding site. Histidines His250 and His280 participate in this process. Although the three‐dimensional structure of Agp1 has been solved at high resolution, the precise position of hydrogen atoms and protonation pattern in the chromophore binding pocket has not been investigated yet. Here, we present protonated structure models of Agp1 in the Pr state involving appropriately placed hydrogen atoms that were generated by hybrid quantum mechanics/molecular mechanics‐ and electrostatic calculations and validated against experimental structural‐ and spectroscopic data. Although the effect of histidine protonation on the vibrational spectra is weak, our results favor charge neutral H250 and H280 both protonated at Nε. However, a neutral H250 with a proton at Nε and a cationic H280 may also be possible. Furthermore, the present QM/MM calculations of IR and Raman spectra of Agp1 containing isotope‐labeled BV provide a detailed vibrational assignment of the biliverdin modes in the fingerprint region.     

An opsin shift in rhodopsin: retinal S0-S1 excitation in protein, in solution, and in the gas phase

We considered a series of model systems for treating the photoabsorption of the 11-cis retinal chromophore in the protonated Schiff-base form in vacuum, solutions, and the protein environment. A high computational level, including the quantum mechanical-molecular mechanical (QM/MM) approach for solution and protein was utilized in simulations. The S0-S1 excitation energies in quantum subsystems were evaluated by means of an augmented version of the multiconfigurational quasidegenerate perturbation theory (aug-MCQDPT2) with the ground-state geometry parameters optimized in the density functional theory PBE0/cc-pVDZ approximation. The computed positions of absorption bands lambdamax, 599(g), 448(s), and 515(p) nm for the gas phase, solution, and protein, respectively, are in excellent agreement with the corresponding experimental data, 610(g), 445(s), and 500(p) nm. Such consistency provides a support for the formulated qualitative conclusions on the role of the chromophore geometry, environmental electrostatic field, and the counterion in different media. An essentially nonplanar geometry conformation of the chromophore group in the region of the C14-C15 bond was obtained for the protein, in particular, owing to the presence of the neighboring charged amino acid residue Glu181. Nonplanarity of the C14-C15 bond region along with the influence of the negatively charged counterions Glu181 and Glu113 are found to be important to reproduce the spectroscopic features of retinal chromophore inside the Rh cavity. Furthermore, the protein field is responsible for the largest bond-order decrease at the C11-C12 double bond upon excitation, which may be the reason for the 11-cis photoisomerization specificity.     

Prediction of cyclohexane-water distribution coefficients for the SAMPL5 data set using molecular dynamics simulations with the OPLS-AA force field

All-atom molecular dynamics simulations were used to predict water-cyclohexane distribution coefficients \(D_{cw}\) of a range of small molecules as part of the SAMPL5 blind prediction challenge. Molecules were parameterized with the transferable all-atom OPLS-AA force field, which required the derivation of new parameters for sulfamides and heterocycles and validation of cyclohexane parameters as a solvent. The distribution coefficient was calculated from the solvation free energies of the compound in water and cyclohexane. Absolute solvation free energies were computed by an established protocol using windowed alchemical free energy perturbation with thermodynamic integration. This protocol resulted in an overall root mean square error in \(\log D_{cw}\) of almost 4 log units and an overall signed error of ?3 compared to experimental data. There was no substantial overall difference in accuracy between simulating in NVT and NPT ensembles. The signed error suggests a systematic error but the experimental \(D_{cw}\) data on their own are insufficient to uncover the source of this error. Preliminary work suggests that the major source of error lies in the hydration free energy calculations.     

适用于TATB,RDX,HMX含能材料的全原子力场的建立与验证

报道一个适用于三种常见的含能材料分子三硝基三氨基苯(TATB),环三亚甲基三硝胺(RDX),环四亚甲基四硝胺(HMX)的全原子力场.力场采用广泛使用的力场函数形式,其中键参数通过拟合量子化学密度泛函计算的数据获得,电荷参数和范德华参数通过拟合相应的分子晶体的物理性质(密度和升华焓)优化得到.通过计算分子和分子晶体的性质显示该力场可以用来准确地预测分子结构、分子振动频率和分子晶体的晶胞参数、密度和升华焓.进一步的验证显示该力场可用来较为准确地预测分子晶体的状态方程和机械模量.