Coupled cluster calculation of the n --> pi* electronic transition of acetone in aqueous solution

The combined linear response coupled cluster/molecular mechanics (CC/MM) scheme including mutual polarization effects in the coupling Hamiltonian is applied together with supermolecular CC methods to the study of the gas-to-aqueous solution blue shift of the n --> pi* excitation energy in acetone. The aug-cc-pVDZ basis set is found to be adequate for the calculation of this excitation energy. In the condensed phase, the shift in the excitation energy is obtained by statistical averaging over 800 solute-solvent configurations extracted from a molecular dynamics simulation. We find the shift to be around 1100-1200 cm(-1) depending on the specific model used to describe solvent polarization. The importance of including explicit polarization in both the molecular dynamics simulation as well as the CC/MM calculations is emphasized. Furthermore, the significant dependence of the excitation energy on the CO bond length of acetone is discussed.     

Statistical mechanically averaged molecular properties of liquid water calculated using the combined coupled cluster/molecular dynamics method

Liquid water is investigated theoretically using combined molecular dynamics (MD) simulations and accurate electronic structure methods. The statistical mechanically averaged molecular properties of liquid water are calculated using the combined coupled cluster/molecular mechanics (CC/MM) method for a large number of configurations generated from MD simulations. The method includes electron correlation effects at the coupled cluster singles and doubles level and the use of a large correlation consistent basis set. A polarizable force field has been used for the molecular dynamics part in both the CC/MM method and in the MD simulation. We describe how the methodology can be optimized with respect to computational costs while maintaining the quality of the results. Using the optimized method we study the energetic properties including the heat of vaporization and electronic excitation energies as well as electric dipole and quadrupole moments, the frequency dependent electric (dipole) polarizability, and electric-field-induced second harmonic generation first and second hyperpolarizabilities. Comparisons with experiments are performed where reliable data are available. Furthermore, we discuss the important issue on how to compare the calculated microscopic nonlocal properties to the experimental macroscopic measurements.     

Quantum molecular mechanics—a noniterative procedure for the fast Ab Initio calculation of closed shell systems

In this article, we advance the foundations of a strategy to develop a molecular mechanics method based not on classical mechanics and force fields but entirely on quantum mechanics and localized electron‐pair orbitals, which we call quantum molecular mechanics (QMM). Accordingly, we introduce a new manner of calculating Hartree–Fock ab initio wavefunctions of closed shell systems based on variationally preoptimized nonorthogonal electron pair orbitals constructed by linear combinations of basis functions centered on the atoms. QMM is noniterative and requires only one extremely fast inversion of a single sparse matrix to arrive to the one‐particle density matrix, to the electron density, and consequently, to the ab initio electrostatic potential around the molecular system, or cluster of molecules. Although QMM neglects the smaller polarization effects due to intermolecular interactions, it fully takes into consideration polarization effects due to the much stronger intramolecular geometry distortions. For the case of methane, we show that QMM was able to reproduce satisfactorily the energetics and polarization effects of all distortions of the molecule along the nine normal modes of vibration, well beyond the harmonic region. We present the first practical applications of the QMM method by examining, in detail, the cases of clusters of helium atoms, hydrogen molecules, methane molecules, as well as one molecule of HeH⁺ surrounded by several methane molecules. We finally advance and discuss the potentialities of an exact formula to compute the QMM total energy, in which only two center integrals are involved, provided that the fully optimized electron‐pair orbitals are known. © 2012 Wiley Periodicals, Inc.     

Conformational simulations of aqueous solvated alpha-conotoxin GI and its single disulfide analogues using a polarizable force field model

The solution conformation of alpha-conotoxin GI and its two single disulfide analogues are simulated using a polarizable force field in combination with the molecular fragmentation quantum chemical calculation. The polarizability is explicitly described by allowing the partial charges and fragment dipole moments to be variables, with values coming from the linear-scaling energy-based molecular fragmentation calculations at the B3LYP/6-31G(d) level. In comparison with the full quantum chemical calculations, the fragmentation approaches can yield precise ground-state energies, dipole moments, and static polarizabilities for peptides. The B3LYP/6-31G(d) charges and fragment-centered dipole moments are introduced in calculations of electrostatic terms in both AmberFF03 and OPLS force fields. Our test calculations on the gas-phase glucagon (PDB code: 1gcn) and solvated alpha-conotoxin GI (PDB code: 1not) demonstrate that the present polarization model is capable of describing the structural properties (such as the relative conformational energies, intramolecular hydrogen bonds, and disulfide bonds) with accuracy comparable to some other polarizable force fields (ABEEM/MM and OPLS-PFF) and the quantum mechanics/molecular mechanics (QM/MM) hybrid model. The employment of fragment-centered dipole moments in calculations of dipole-dipole interactions can save computational time in comparison with those polarization models using atom-centered dipole moments without much loss of accuracy. The molecular dynamics simulations using the polarizable force field demonstrate that two single disulfide GI analogues are more flexible and less structured than the native alpha-conotoxin GI, in agreement with NMR experiments. The polarization effect is important in simulations of the folding/unfolding process of solvated proteins.     

Efficient Calculation of Absorption Spectra in Solution: Approaches for Selecting Representative Solvent Configurations and for Reducing the Number of Explicit Solvent Molecules

Dye-sensitized solar cells(DSSCs) are one of the most promising renewable energy technologies. Charge transfer and charge transport are pivotal processes in DSSCs, which govern solar energy capture and conversion. These processes can be probed using modern electronic structure methods. Because of the heterogeneity and complexity of the local environment of a chromophore in DSSCs(such as solvatochromism and chromophore aggregation), a part of the solvation environment should be treated explicitly during the calculation. However, because of the high computational cost and unfavorable scaling with the number of electrons of high-level quantum mechanical methods, approaches to explicitly treat the local environment need careful consideration. Two problems must be tackled to reduce computational cost. First, the number of configurations representing the solvent distribution should be limited as much as possible. Second, the size of the explicit region should be kept relatively small. The purpose of this study is to develop efficient computational approaches to select representative configurations and to limit the explicit solvent region to reduce the computational cost for later(higher-level) quantum mechanical calculations. For this purpose, an ensemble of solvent configurations around a 1-methyl-8-oxyquinolinium betaine(QB) dye molecule was generated using Monte Carlo simulations and molecular mechanics force fields. Then, a fitness function was developed using data from inexpensive electronic structure calculations to reduce the number of configurations. Specific solvent molecules were also selected for explicit treatment based on a distance criterion, and those not selected were treated as background charges. The configurations and solvent molecules selected proved to be good representatives of the entire ensemble; thus, expensive electronic structure calculations need to be performed only on this subset of the system, which significantly reduces the computational cost.     

Molecular binding at gold transport interfaces. III. Field dependence of electronic properties

The behavior of the electronic structure in a metal/molecular/metal junction as a function of the applied electric field is studied using density functional methods. Although the calculations reported here do not include the electrode bulk, or intermolecular interactions, and do not permit actual transport to occur, nevertheless they illuminate the charging, energy shift, polarization and orbital occupation changes in the molecular junction upon the application of a static electric field. Specifically, external electric fields generally induce polarization localization on the two cluster ends. The HOMO/LUMO gap usually decreases and, for large enough fields, energy levels can cross, which presages a change of electronic state and, if found in molecular electronic circuits, a change in transmission. The calculations also show changes in the geometry both of the molecule and the molecule/cluster interface upon application of the electric field. These effects should be anticipated in whole circuit studies.     

Molecular dynamics simulations of methane hydrate using polarizable force fields

Molecular dynamics simulations of methane hydrate have been carried out using the polarizable AMOEBA and COS/G2 force fields. Properties calculated include the temperature dependence of the lattice constant, the OC and OO radial distribution functions, and the vibrational spectra. Both the AMOEBA and COS/G2 force fields are found to successfully account for the available experimental data, with overall somewhat better agreement with experiment being found for the AMOEBA model. Comparison is made with previous results obtained using TIP4P and SPC/E effective two-body force fields and the polarizable TIP4P-FQ force field, which allows for in-plane polarization only. Significant differences are found between the properties calculated using the TIP4P-FQ model and those obtained using the other models, indicating an inadequacy of restricting explicit polarization to in-plane only.     

Theoretical studies of the Wilcox molecular torsion balance. Is the edge-to-face aromatic interaction important?

[formula: see text] Molecular mechanics calculations with several different force fields and the GB/SA solvation model were carried out for the molecular torsion balance developed by Wilcox et al. to investigate the intramolecular nonbonded interactions between two aromatic rings. The preference is found to arise from a balance between intramolecular van der Waals interactions and solvation effects, with the latter favoring the unfolded conformation.     

Solvation and ion-pairing properties of the aqueous sulfate anion: explicit versus effective electronic polarization

We assessed the relative merits of two approaches for including polarization effects in classical force fields for the sulfate anion. One of the approaches is the explicit shell model for atomic polarization and the other is an implicit dielectric continuum representation of the electronic polarization, wherein the polarizability density is spatially uniform. Both the solvation and ion association properties of sulfate were considered. We carried out an ab initio molecular dynamics simulation for a single sulfate anion in aqueous solution to obtain a benchmark for the solvation structure. For the ion-pairing properties, the models were compared to experimental thermodynamic data through Kirkwood-Buff theory, which relates the integrals of the pair correlation functions to measurable properties. While deficiencies were found for both of the approaches, the continuum polarization model was not systematically worse than the shell model. The shell model was found to give a more structured solution than the continuum polarization model, both with respect to solvation and ion pairing.     

Development of a polarizable force field for proteins via ab initio quantum chemistry: first generation model and gas phase tests

We present results of developing a methodology suitable for producing molecular mechanics force fields with explicit treatment of electrostatic polarization for proteins and other molecular system of biological interest. The technique allows simulation of realistic-size systems. Employing high-level ab initio data as a target for fitting allows us to avoid the problem of the lack of detailed experimental data. Using the fast and reliable quantum mechanical methods supplies robust fitting data for the resulting parameter sets. As a result, gas-phase many-body effects for dipeptides are captured within the average RMSD of 0.22 kcal/mol from their ab initio values, and conformational energies for the di- and tetrapeptides are reproduced within the average RMSD of 0.43 kcal/mol from their quantum mechanical counterparts. The latter is achieved in part because of application of a novel torsional fitting technique recently developed in our group, which has already been used to greatly improve accuracy of the peptide conformational equilibrium prediction with the OPLS-AA force field.1 Finally, we have employed the newly developed first-generation model in computing gas-phase conformations of real proteins, as well as in molecular dynamics studies of the systems. The results show that, although the overall accuracy is no better than what can be achieved with a fixed-charges model, the methodology produces robust results, permits reasonably low computational cost, and avoids other computational problems typical for polarizable force fields. It can be considered as a solid basis for building a more accurate and complete second-generation model.     

Urea: an ab initio and force field study of the gas and solid phases

We have studied the gaseous and solid phases of urea using both quantum mechanics calculation and force field simulation methods. Our ab initio calculations confirmed experimental observations that urea structure is planar in the crystal, but nonplanar in the gas phase. Based on electron structure analysis, we suggest that the significant difference between these two structures in different environments can be qualitatively explained by two resonance structures. The planar structure is more polarized than the nonplanar one, and the former is stabilized in the solid phases due to strong electrostatic interactions. We found classical force field method is incapable to represent such strong polarization effect. Using molecular dynamics simulations with a force field optimized for condensed phases, we calculated the crystalline structures of urea in the temperature range of 12 to 293 K. The densities as well as cell parameters are within 2% deviation from the experimental data in the temperature range.     

Using PC clusters to evaluate the transferability of molecular mechanics force fields for proteins

The transferability of molecular mechanics parameters derived for small model systems to larger biopolymers such as proteins can be difficult to assess. Even for small peptides, molecular dynamics simulations are typically too short to sample structures significantly different than initial conformations, making comparison to experimental data questionable. We employed a PC cluster to generate large numbers of native and non-native conformations for peptides with experimentally measured structural data, one predominantly helical and the other forming a beta-hairpin. These atomic-detail sets do not suffer from slow convergence, and can be used to rapidly evaluate important force field properties. In this case a suspected bias toward alpha-helical conformations in the ff94 and ff99 force fields distributed with the AMBER package was verified. The sets provide critical feedback not only on force field transferability, but may also predict modifications for improvement. Such predictions were used to modify the ff99 parameter set, and the resulting force field was used to test stability and folding of model peptides. Structural behavior during molecular dynamics with the modified force field is found to be very similar to expectations, suggesting that these basis sets of conformations may themselves have significant transferability among force fields. We continue to improve and expand this data set and plan to make it publicly accessible. The calculations involved in this process are trivially parallel and can be performed using inexpensive personal computers with commodity components.     

The role of intermolecular hydrogen bond on dielectric properties in hydrogen-bonded material 5-bromo-9-hydroxyphenalenone: theoretical investigation

Dielectric properties of the hydrogen-bonded material, 5-bromo-9-hydroxyphenalenone (C(13)H(7)O(2)Br; BrHPLN), are investigated theoretically by means of electronic structure calculations and Monte Carlo simulations. The density functional calculations of BrHPLN crystals have revealed that the polarization per one molecule can be about 1.7 times larger than that of the isolated monomer. It is also found that there exists significant electron density (0.01 e bohr(-3)) in an intermolecular C-H···O region, which, together with the interatomic distances of 2.39 ? for H···O and 3.34 ? for C···O, suggests the existence of intermolecular weak hydrogen bonding that may enhance the molecular polarization. The induced polarization effects in various intermolecular configurations are evaluated with the Fragment Molecular Orbital method. In addition to the π-π stacking interactions, two types of "in plane" intermolecular weak hydrogen-bonding configurations are found to affect the molecular dipole moment most significantly. These effects are efficiently included in a Monte Carlo simulation method in terms of "dipole corrections" as functions of both the intermolecular arrangements and the intramolecular proton configurations. The application to the dielectric phase transition of a BrHPLN crystal shows that the dipole corrections almost double the transition temperature, toward better agreement with experiments, and qualitatively affect the temperature dependence of the dielectric constant. Discussions are given to support that the results will remain adequate and consistent even after explicit inclusion of the quantum tunneling effects.     

Computation of induced dipoles in molecular mechanics simulations using graphics processors

In this work, we present a tentative step toward the efficient implementation of polarizable molecular mechanics force fields with GPU acceleration. The computational bottleneck of such applications is found in the treatment of electrostatics, where higher-order multipoles and a self-consistent treatment of polarization effects are needed. We have implemented a GPU accelerated code, based on the Tinker program suite, for the computation of induced dipoles. The largest test system used shows a speedup factor of over 20 for a single precision GPU implementation, when comparing to the serial CPU version. A discussion of the optimization and parametrization steps is included. Comparison between different graphic cards and CPU-GPU embedding is also given. The current work demonstrates the potential usefulness of GPU programming in accelerating this field of applications.     

Effect of polarization on the opsin shift in rhodopsins. 1. A combined QM/QM/MM model for bacteriorhodopsin and pharaonis sensory rhodopsin II

The optical and IR-spectroscopic properties of the protonated Schiff base of retinal are highly sensitive to the electrostatic environment. This feature makes retinal a useful probe to study structural differences and changes in rhodopsins. It also raises an interest to theoretically predict the spectroscopic response to mutation and structural evolution. Computational models appropriate for this purpose usually combine sophisticated quantum mechanical (QM) methods with molecular mechanics (MM) force fields. In an effort to test and improve the accuracy of these QM/MM models, we consider in this article the effects of polarization and inter-residual charge transfer within the binding pocket of bacteriorhodopsin (bR) and pharaonis sensory rhodopsin II (psRII, also called pharaonis phoborhodopsin, ppR) on the excitation energy using an ab initio QM/QM/MM approach. The results will serve as reference for assessing empirical polarization models in a consecutive article.     

Ab initio molecular dynamics study of formate ion hydration

We perform ab initio molecular dynamics simulations of the aqueous formate ion. The mean number of water molecules in the first solvation shell, or the hydration number, of each formate oxygen is found to be consistent with recent experiments. Our ab initio pair correlation functions, however, differ significantly from many classical force field results and hybrid quantum mechanics/molecular mechanics predictions. They yield roughly one less hydrogen bond between each formate oxygen and water than force field or hybrid methods predict. Both the BLYP and PW91 exchange correlation functionals give qualitatively similar results. The time dependence of the hydration numbers are examined, and Wannier function techniques are used to analyze electronic configurations along the molecular dynamics trajectory.