Simulations of liquid ammonia based on the combined quantum mechanical/molecular mechanical (QM/MM) approach

Two combined quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulations, namely, HF/MM and B3LYP/MM, have been performed to investigate the local structure and dynamics of liquid ammonia. The most interesting region, a sphere containing a central reference molecule and all its nearest surrounding molecules (first coordination shell), was treated by the Hartree-Fock (HF) and hybrid density functional B3LYP methods, whereas the rest of the system was described by the classical pair potentials. On the basis of both HF and B3LYP methods, it is observed that the hydrogen bonding in this peculiar liquid is weak. The structure and dynamics of this liquid are suggested to be determined by the steric packing effects, rather than by the directional hydrogen bonding interactions. Compared to previous empirical as well as Car-Parrinello (CP) molecular dynamics studies, our QM/MM simulations provide detailed information that is in better agreement with experimental data.     

Correlation effects on the structure and dynamics of the H3O+ hydrate: B3LYP/MM and MP2/MM MD simulations

Two combined quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations, namely B3LYP/MM and MP2/MM, have been performed to investigate the possible influence of electron correlation on the structure and dynamics of the H(3)O(+) hydrate. In comparison to the previously published HF/MM results, both B3LYP/MM and MP2/MM simulations clearly reveal stronger H(3)O(+)-water hydrogen bond interactions, which are reflected in a slightly greater compactness of the H(3)O(+) hydrate. However, the B3LYP/MM simulation, although providing structural details very close to the MP2/MM data, shows an artificially slow dynamic nature of some first shell water molecules as a consequence of the formation of a long-lived H(3)O(+)···H(2)O hydrogen bonding structure.     

A combined QM/MM molecular dynamics simulations study of nitrate anion (NO3-) in aqueous solution

The structural and dynamical properties of NO3- in dilute aqueous solution have been investigated by means of two combined quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulations, namely HF/MM and B3LYP/MM, in which the ion and its surrounding water molecules were treated at HF and B3LYP levels of accuracy, respectively, using the DZV+ basis set. On the basis of both HF and B3LYP methods, a well-defined first hydration shell of NO3- is obtainable, but the shell is quite flexible and the hydrogen-bond interactions between NO3- and water are rather weak. With respect to the detailed analysis of the geometrical arrangement and vibrations of NO3-, the experimentally observed solvent-induced symmetry breaking of the ion is well reflected. In addition, the dynamical information, i.e., the bond distortions and shifts in the corresponding bending and stretching frequencies as well as the mean residence time of water molecules surrounding the NO3- ion, clearly indicates the "structure-breaking" ability of this ion in aqueous solution. From a methodical point of view it seems that both the HF and B3LYP methods are not too different in describing this hydrated ion by means of a QM/MM simulation. However, the detailed analysis of the dynamics properties indicates a better suitability of the HF method compared to the B3LYP-DFT approach.     

Cu(II) in liquid ammonia: an approach by hybrid quantum-mechanical/molecular-mechanical molecular dynamics simulation.

To investigate the solvation structure of the Cu(II) ion in liquid ammonia, ab initio quantum-mechanical/molecular-mechanical (QM/MM) molecular dynamics (MD) simulations were carried out at Hartree Fock (HF) and hybrid density functional theory (B3 LYP) levels. A sixfold-coordinated species was found to be predominant in the HF case whereas five- and sixfold-coordinated complexes were obtained in a ratio 2:1 from the B3 LYP simulation. In contrast to hydrated Cu(II), which exhibits a typical Jahn-Teller distortion, the geometrical arrangement of ligand molecules in the case of ammonia can be described as a [2 + 4] ([2 + 3]) configuration with 4 (3) elongated copper-nitrogen bonds. First shell solvent exchange reactions at picosecond rate took place in both HF and B3 LYP simulations, again in contrast to the more stable sixfold-coordinated hydrate. NH3 ligands apparently lead to strongly accelerated dynamics of the Cu(II) solvate due to the "inverse" [2 + 4] structure with its larger number of elongated copper-ligand bonds. Several dynamical properties, such as mean ligand residence times or ion-ligand stretching frequencies, prove the high lability of the solvated complex.     

Revisiting the structure and dynamics of hydrated Cd2+ in aqueous solutions: Insights from the RI-SCS-MP2/MM molecular dynamics simulation

The spin component scale MP2/molecular mechanics molecular dynamics simulation investigated the hydration shell formation and hydrated Cd²⁺ dynamics in the water environment. At the first hydration shell, six water molecules with 2.27 Å for the average distance between water and Cd²⁺. Dynamical properties were analyzed by computing the water molecule's mean residence time (MRT) in its first and second hydration shells. The MRT of each shell was determined to be 31.8 and 1.92 ps, suggesting the strong influence of Cd²⁺ in the first hydration shell. The second shell was labile, with an average number of water molecules being 18. Despite the strong interaction between Cd²⁺ and water molecules in the first shell, the influence of ions in the second hydration shell remained weak.     

Quantum mechanical charge field molecular dynamics simulation of the TiO2+ ion in aqueous solution

Structural and dynamical properties of the TiO(2+) ion in aqueous solution have been investigated by using the new ab initio quantum mechanical charge field (QMCF) molecular dynamics (MD) formalism, which does not require any other potential functions except those for solvent-solvent interactions. Both first and second hydration shell have been treated at Hartree-Fock (HF) quantum mechanical level. A Ti-O bond distance of 1.5 A was observed for the [Ti=O](2+) ion. The first hydration shell of the ion shows a varying coordination number ranging from 5 to 7, five being the dominant one and representing one axial and four equatorial water molecules directly coordinated to Ti, which are located at 2.3 A and 2.1 A, respectively. The flexibility in the coordination number reflects the fast exchange processes, which occur only at the oxo atom, where water ligands are weakly bound through hydrogen bonds. Considering the first shell hydration, the composition of the TiO(2+) hydrate can be characterized as [(H(2)O)(0.7)(H(2)O)(4) (eq)(H(2)O)(ax)](2+). The second shell consists in average of 12 water molecules located at a mean distance of 4.4 A. Several other structural parameters such as radial and angular distribution functions and coordination number distributions were analyzed to fully characterize the hydration structure of the TiO(2+) ion in aqueous solution. For the dynamics of the TiO(2+) ion, different sets of dynamical parameters such as Ti=O, Ti-O(eq), and Ti-O(ax) stretching frequencies and ligands' mean residence times were evaluated. During the simulation time of 15 ps, 3 water exchange processes in the first shell were observed at the oxo atom, corresponding to a mean residence time of 3.6 ps. The ligands' mean residence time for the second shell was determined as 3.5 ps.     

Characteristics of CO3(2-)-water hydrogen bonds in aqueous solution: insights from HF/MM and B3LYP/MM MD simulations

Two combined quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulations, namely HF/MM and B3LYP/MM, have been performed to investigate the local hydration structure and dynamics of carbonate (CO(3)(2-)) in dilute aqueous solution. With respect to the QM/MM scheme, the QM region, which contains the CO(3)(2-) and its surrounding water molecules, was treated at HF and B3LYP levels of accuracy, respectively, using the DZV+ basis set, while the rest of the system is described by classical MM potentials. For both the HF/MM and B3LYP/MM simulations, it is observed that the hydrogen bonds between CO(3)(2-) oxygens and their nearest-neighbor waters are relatively strong, i.e., compared to water-water hydrogen bonds in the bulk, and that the first shell of each CO(3)(2-) oxygen atom somewhat overlaps with the others, which allows migration of water molecules among the coordinating sites to exist. In addition, it is observed that first-shell waters are either "loosely" or "tightly" bound to the respective CO(3)(2-) oxygen atoms, leading to large fluctuations in the number of first-shell waters, ranging from 1 to 6 (HF/MM) and 2 to 7 (B3LYP/MM), with the prevalent value of 3. Upon comparing the HF and B3LYP methods in describing this hydrated ion, the latter is found to overestimate the hydrogen-bond strength in the CO(3)(2-)-water complexes, resulting in a slightly more compact hydration structure at each of the CO(3)(2-) oxygens.     

Conformational analysis of methylphenidate: comparison of molecular orbital and molecular mechanics methods

Summary Methylphenidate (MP) binds to the cocaine binding site on the dopamine transporter and inhibits reuptake of dopamine, but does not appear to have the same abuse potential as cocaine. This study, part of a comprehensive effort to identify a drug treatment for cocaine abuse, investigates the effect of choice of calculation technique and of solvent model on the conformational potential energy surface (PES) of MP and a rigid methylphenidate (RMP) analogue which exhibits the same dopamine transporter binding affinity as MP. Conformational analysis was carried out by the AM1 and AM1/SM5.4 semiempirical molecular orbital methods, a molecular mechanics method (Tripos force field with the dielectric set equal to that of vacuum or water) and the HF/6-31G* molecular orbital method in vacuum phase. Although all three methods differ somewhat in the local details of the PES, the general trends are the same for neutral and protonated MP. In vacuum phase, protonation has a distinctive effect in decreasing the regions of space available to the local conformational minima. Solvent has little effect on the PES of the neutral molecule and tends to stabilize the protonated species. The random search (RS) conformational analysis technique using the Tripos force field was found to be capable of locating the minima found by the molecular orbital methods using systematic grid search. This suggests that the RS/Tripos force field/vacuum phase protocol is a reasonable choice for locating the local minima of MP. However, the Tripos force field gave significantly larger phenyl ring rotational barriers than the molecular orbital methods for MP and RMP. For both the neutral and protonated cases, all three methods found the phenyl ring rotational barriers for the RMP conformers/invertamers (denoted as cte, tte, and cta) to be: cte, tte> MP > cta. Solvation has negligible effect on the phenyl ring rotational barrier of RMP. The B3LYP/6-31G* density functional method was used to calculate the phenyl ring rotational barrier for neutral MP and gave results very similar to those of the HF/6-31G* method.     

Molecular dynamics, density functional and second-order Møller–Plesset theory study of the structure and conformation of acetylcholine in vacuo and in solution

 Molecular mechanics minimizations based on the CVFF force field and molecular dynamics simulation for a time of 2.5 ns were performed to examine the conformational behaviour and the molecular motion of acetylcholine in vacuo and in aqueous solution. Five low-lying conformations, namely the TT, TG, GG, G*G and GT, were obtained from molecular mechanics computations with the GT structure as the absolute minimum. Molecular dynamics trajectories in vacuo and in water show that only four (GT, GG, G*G and TG) and three (TG, TT and GT) conformations are present in the simulation time, respectively. Density functional B3LYP and second-order M?ller–Plesset (MP2) methods were then used to study all the five lowest-lying conformers of acetylcholine neurotransmitter in vacuo and in water by the polarizable continuum model approach. The B3LYP and MP2 computations show that in the gas phase all minima lie in a narrow range of energy with the G*G conformer as the most stable one. The relative minima GG, GT, TG and TT are located at 1.1 (3.3), 1.8 (4.2), 2.1 (4.5) and 4.3 (7.3) kcal/mol above the absolute one at the B3LYP (MP2) level. The preferred conformation in water is the TG. Solvation reduces the relative energy differences between the five minima in both computations. Received: 4 April 2001 / Accepted: 5 July 2001 / Published online: 30 October 2001     

Structure and dynamics of high-spin Ru in aqueous solution: Ab initio QM/MM molecular dynamics simulation

The structural and dynamical properties of high-spin Ru²⁺ in aqueous solution have been theoretically studied using molecular dynamics (MD) simulations. The conventional MD simulation based on pair potentials gives the overestimated average first shell coordination number of 9, whereas the value of 5.9 was observed when the three-body corrected function was included. A combined ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulation has been performed to take into account the many-body effects on the hydration shell structure of Ru²⁺. The most important region, the first hydration shell, was treated by ab initio quantum mechanics at UHF level using the SBKJC VDZ ECP basis set for Ru²⁺ and the 6-31G^∗ basis sets for water. An exact coordination number of 6 for the first hydration shell was obtained from the QM/MM simulation. The QM/MM simulation predicts the average Ru²⁺–O distance of 2.42 Å for the first hydration shell, whereas the values of 2.34 and 2.46 Å are resulted from the pair potentials without and with the three-body corrected simulations, respectively. Several other structural properties representing position and orientation of the solvate molecules were evaluated for describing the hydration shell structure of the Ru²⁺ ion in dilute aqueous solution. A mean residence time of 7.1 ps was obtained for water ligands residing in the second hydration shell.     

Structure and dynamics of the CrIII ion in aqueous solution: Ab initio QM/MM molecular dynamics simulation

Structural and dynamical properties of the Cr(III) ion in aqueous solution have been investigated using a combined ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulation. The hydration structure of Cr(III) was determined in terms of radial distribution functions, coordination numbers, and angular distributions. The QM/MM simulation gives coordination numbers of 6 and 15.4 for the first and second hydration shell, respectively. The first hydration shell is kinetically very inert but by no means rigid and variations of the first hydration shell geometry lead to distinct splitting in the vibrational spectra of Cr(H(2)O)(6) (3+). A mean residence time of 22 ps was obtained for water ligands residing in the second hydration shell, which is remarkably shorter than the experimentally estimated value. The hydration energy of -1108 +/- 7 kcal/mol, obtained from the QM/MM simulation, corresponds well to the experimental hydration enthalpy value.     

DTMM and COSMIC molecular mechanics parameters for alkylsilanes

Harmonic DTMM and COSMIC molecular mechanical force fields were extended to cover aliphatic silanes. Structures of the thirty-five molecules were examined and they generally fit approximately within experimental error. For these, root mean square deviations between the calculated and the experimentally determined geometrical data were found to be less than 0.05 Å and 1.7 deg. for bond lengths and bond angles, respectively. The accuracy of these force fields was also verified in comparison with the other force fields (MM2, MM3), semi-empirical (PM3), ab initio (HF,MP2) and density functional (B3LYP, BP86) quantum chemical methods. The relative stability of the seventeen conformations of seven simple molecules was investigated and the limitations of the DTMM software is discussed.     

Hydration shell structure and dynamics of curium(III) in aqueous solution: first principles and empirical studies

Results of ab initio molecular dynamics (AIMD), quantum mechanics/molecular mechanics (QM/MM), and classical molecular dynamics (CMD) simulations of Cm(3+) in liquid water at a temperature of 300 K are reported. The AIMD simulation was based on the Car-Parrinello MD scheme and GGA-PBE formulation of density functional theory. Two QM/MM simulations were performed by treating Cm(3+) and the water molecules in the first shell quantum mechanically using the PBE (QM/MM-PBE) and the hybrid PBE0 density functionals (QM/MM-PBE0). Two CMD simulations were carried out using ab initio derived pair plus three-body potentials (CMD-3B) and empirical Lennard-Jones pair potential (CMD-LJ). The AIMD and QM/MM-PBE simulations predict average first shell hydration numbers of 8, both of which disagree with recent experimental EXAFS and TRLFS value of 9. On the other hand, the average first shell hydration numbers obtained in the QM/MM-PBE0 and CMD simulations was 9, which agrees with experiment. All the simulations predicted an average first shell and second shell Cm-O bond distance of 2.49-2.53 ? and 4.67-4.75 ? respectively, both of which are in fair agreement with corresponding experimental values of 2.45-2.48 and 4.65 ?. The geometric arrangement of the 8-fold and 9-fold coordinated first shell structures corresponded to the square antiprism and tricapped trigonal prisms, respectively. The second shell hydration number for AIMD QM/MM-PBE, QM/MM-PBE0, CMD-3B, and CMD-LJ, were 15.8, 17.2, 17.7, 17.4, and 16.4 respectively, which indicates second hydration shell overcoordination compared to a recent EXAFS experimental value of 13. Save the EXAFS spectra CMD-LJ simulation, all the computed EXAFS spectra agree fairly well with experiment and a clear distinction could not be made between configurations with 8-fold and 9-fold coordinated first shells. The mechanisms responsible for the first shell associative and dissociative ligand exchange in the classical simulations have been analyzed. The first shell mean residence time was predicted to be on the nanosecond time scale. The computed diffusion constants of Cm(3+) and water are in good agreement with experimental data.     

De novo prediction of the ground state structure of transition metal complexes using semiempirical and ab initio quantum mechanics. Coordination isomerism

The ground state coordination isomers for 30 different trigonal bipyramidal transition metal complexes have been predicted using different levels of quantum mechanics: semiempirical (PM3(tm)), ab initio (MP2//HF), pure (BPW91) and hybrid (B3PW91) density functional theory (DFT) methods. For species where these methods failed to reproduce crystallographic data, hybrid quantum mechanics/molecular mechanics (QM/MM) methods were used to study more exact experimental models. Literature deficiencies regarding ground state multiplicity of these species were supplemented by spin predictions using previously tested PM3(tm) methods. Geometry optimization calculations were performed for each possible coordination isomer. The predicted ground state minima provided by the different methods are compared to each other and with crystallographic data. Pure DFT functionals outperformed hybrid functionals and MP2//HF. The very rapid PM3(tm) parameterization method provided accurate predictions in comparison to other levels of theory. An integrated MM/PM3(tm)/DFT de novo scheme accurately reproduced crystallographic data for species where the individual methods failed.     

The performance of different density functional methods in the calculation of molecular structures and vibrational spectra of platinum(II) antitumor drugs: cisplatin and carboplatin

A comparison of eight density functional models for predicting the molecular structures, vibrational frequencies, infrared intensities, and Raman scattering activities of platinum(II) antitumor drugs, cisplatin and carboplatin, is reported. Methods examined include the pure density functional protocols (G96LYP, G96PW91, modified mPWPW and original PW91PW91), one‐parameter hybrid approaches (mPW1PW and mPW1LYP), and three‐parameter hybrid models (B3LYP and B3PW91), as well as the HF and MP2 levels of theory. Different effective core potentials (ECPs) and several basis sets are considered. The theoretical results are discussed and compared with the experimental data. It is remarkable that the mPW1PW protocol introduced by Adamo and Barone [J Chem Phys 1998, 108, 664], is clearly superior to all the remaining density functional methods (including B3LYP). The geometry and vibrational frequencies of cisplatin and carboplatin calculated with the mPW1PW method, and the ECP of Hay and Wadt (LanL2DZ basis set) are in better agreement with experiment than those obtained with the MP2 method. The use of more elaborated ECP and the enlargements of basis sets do not significantly improve the results. A clear‐cut assignments of the platinum‐ligand vibrations in cisplatin and carboplatin are presented. It is concluded that mPW1PW is the new reliable method, which can be used in predicting molecular structures and vibrational spectra of large coordination compounds containing platinum(II). © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 901–912, 2001     

Charge distributions for molecular dynamics simulations from self-consistent polarization method

Partial atomic charges are important force field parameters. They are usually computed by applying quantum-chemical calculations and the assumed population scheme. In this study polarization consistent scheme of deriving a charge distribution inside solute molecule is proposed. The environment effect is explicitly taken into account by distributing solvent molecules around the solute target. The performed analysis includes a few computational schemes (HF, MP2, B3LYP, and M026X), basis sets (cc-pvnz, n = 2, 3, …, 6), and electrostatically derived charge distributions (KS, CHELP, CHELPG, and HLY). It is demonstrated that the environment effect is very important and cannot be disregarded. The second solvation shell should be included to achieve the charge convergence. Huge corrections to charge distribution are due to induction and dispersion. The B3LYP/cc-pvqz level of theory is recommended for deriving the charges within self-consistent polarization scheme.     

Ab initio vs molecular mechanics thermochemistry: homocubanes

The standard enthalpies of formation and strain energies for a series of homocubanes have been investigated by high-level ab initio G3(MP2)/B3LYP method. The relative stabilities of isomers are discussed. The comparison is made between the results of ab initio and molecular mechanics methods with the aim of assessing their performances. The usefulness of high-level calculations for generating thermochemical databases of relatively large molecules (e.g. C(11)H(14)) was also demonstrated.