Structure and electronic properties of hydrated mesityl oxide: a sequential quantum mechanics/molecular mechanics approach

The hydration of mesityl oxide (MOx) was investigated through a sequential quantum mechanics/molecular mechanics approach. Emphasis was placed on the analysis of the role played by water in the MOx syn–anti equilibrium and the electronic absorption spectrum. Results for the structure of the MOx–water solution, free energy of solvation and polarization effects are also reported. Our main conclusion was that in gas-phase and in low-polarity solvents, the MOx exists dominantly in syn-form and in aqueous solution in anti-form. This conclusion was supported by Gibbs free energy calculations in gas phase and in-water by quantum mechanical calculations with polarizable continuum model and thermodynamic perturbation theory in Monte Carlo simulations using a polarized MOx model. The consideration of the in-water polarization of the MOx is very important to correctly describe the solute–solvent electrostatic interaction. Our best estimate for the shift of the π–π^* transition energy of MOx, when it changes from gas-phase to water solvent, shows a red-shift of −2,520 ± 90 cm⁻¹, which is only 110 cm⁻¹ (0.014 eV) below the experimental extrapolation of −2,410 ± 90 cm⁻¹. This red-shift of around −2,500 cm⁻¹ can be divided in two distinct and opposite contributions. One contribution is related to the syn → anti conformational change leading to a blue-shift of ~1,700 cm⁻¹. Other contribution is the solvent effect on the electronic structure of the MOx leading to a red-shift of around −4,200 cm⁻¹. Additionally, this red-shift caused by the solvent effect on the electronic structure can by composed by approximately 60 % due to the electrostatic bulk effect, 10 % due to the explicit inclusion of the hydrogen-bonded water molecules and 30 % due to the explicit inclusion of the nearest water molecules.     

Isotope effects in molecular mechanics (MM2). Calculations deuterium compounds

Parameters have been derived so as to enable the inclusion of deuterium in the MM2 molecular mechanics force field. Several compounds were studied and the results are compared with experiment. The results are never qualitatively wrong, but the accuracy ranges from excellent to only fair. They are quite good for hydrocarbons, but less so for ketones.     

Electronic properties of liquid ammonia: a sequential molecular dynamics/quantum mechanics approach

The electronic properties of liquid ammonia are investigated by a sequential molecular dynamics/quantum mechanics approach. Quantum mechanics calculations for the liquid phase are based on a reparametrized hybrid exchange-correlation functional that reproduces the electronic properties of ammonia clusters [(NH3)n; n=1-5]. For these small clusters, electron binding energies based on Green's function or electron propagator theory, coupled cluster with single, double, and perturbative triple excitations, and density functional theory (DFT) are compared. Reparametrized DFT results for the dipole moment, electron binding energies, and electronic density of states of liquid ammonia are reported. The calculated average dipole moment of liquid ammonia (2.05+/-0.09 D) corresponds to an increase of 27% compared to the gas phase value and it is 0.23 D above a prediction based on a polarizable model of liquid ammonia [Deng et al., J. Chem. Phys. 100, 7590 (1994)]. Our estimate for the ionization potential of liquid ammonia is 9.74+/-0.73 eV, which is approximately 1.0 eV below the gas phase value for the isolated molecule. The theoretical vertical electron affinity of liquid ammonia is predicted as 0.16+/-0.22 eV, in good agreement with the experimental result for the location of the bottom of the conduction band (-V 0=0.2 eV). Vertical ionization potentials and electron affinities correlate with the total dipole moment of ammonia aggregates.     

A molecular-orbital-based molecular mechanics approach to study conjugated systems

The Allinger's MM2 program has been extended to calculate conjugated systems including N, O, and S hetero atoms.     

Nuclear magnetic shielding constants of liquid water: insights from hybrid quantum mechanics/molecular mechanics models

We present a gauge-origin independent method for the calculation of nuclear magnetic shielding tensors of molecules in a structured and polarizable environment. The method is based on a combination of density functional theory (DFT) or Hartree-Fock wave functions with molecular mechanics. The method is unique in the sense that it includes three important properties that need to be fulfilled in accurate calculations of nuclear magnetic shielding constants: (i) the model includes electron correlation effects, (ii) the model uses gauge-including atomic orbitals to give gauge-origin independent results, and (iii) the effect of the environment is treated self-consistently using a discrete reaction-field methodology. The authors present sample calculations of the isotropic nuclear magnetic shielding constants of liquid water based on a large number of solute-solvent configurations derived from molecular dynamics simulations employing potentials which treat solvent polarization either explicitly or implicitly. For both the (17)O and (1)H isotropic shielding constants the best predicted results compare fairly well with the experimental data, i.e., they reproduce the experimental solvent shifts to within 4 ppm for the (17)O shielding and 1 ppm for the (1)H shielding.     

Interpretation of nuclear resonant vibrational spectra of rubredoxin using a combined quantum mechanics and molecular mechanics approach

Nuclear resonant vibrational spectra of the reduced and oxidized form of a mutant of rubredoxin from Pyrococcus abyssii were measured and are compared with simulated spectra that were calculated by a combined quantum mechanics (QM) and molecular mechanics (MM) method. Density functional theory was used for the QM level. Calculations were performed for different models of rubredoxin. Realistic spectra were simulated with reduced models that include at least the iron center, the four cysteins coordinating it, and the residues connected to the cysteins together with a QM layer that comprises the first two coordination shells of the iron center. Larger QM layers did not lead to significant changes of the simulated spectra.     

Automated generation of coupled-cluster diagrams: implementation in the multireference state-specific coupled-cluster approach with the complete-active-space reference

An algorithm for generation of the spin-orbital diagrammatic representation, the corresponding algebraical formulas, and the computer code of the coupled-cluster (CC) method with an arbitrary level of the electronic excitations has been developed. The method was implemented in the general case as well as for specific application in the state-specific multireference coupled-cluster theory (SSMRCC) based on the concept of a "formal reference state." The algorithm was tested in SSMRCC calculations describing dissociation of a single bond and in calculations describing simultaneous dissociation of two single bonds--the problem requiring up to six-particle excitations in the CC operator.     

Calculations of heat of solvation by a simple electrostatic approach to molecular interactions

An extremely simple formula to estimate the heat of formation of complexes between anion and a polar molecule or between highly polar systems is presented.The formula is entirelyelectrostatic and the expression used is verified by means of perturbation theory.This formula is test-ed for several ion-molecule and molecule-molecule pairs.It is also applied to estimate the heat ofhydration of simple salts.     

Density functional self-consistent quantum mechanics/molecular mechanics theory for linear and nonlinear molecular properties: Applications to solvated water and formaldehyde

A combined quantum mechanics/molecular mechanics (QM/MM) method is described, where the polarization between the solvent and solute is accounted for using a self-consistent scheme linear in the solvent polarization. The QM/MM method is implemented for calculation of energies and molecular response properties including the calculation of linear and quadratic response functions using the density-functional theory (DFT) and the Hartree-Fock (HF) theory. Sample calculations presented for ground-state energies, first-order ground-state properties, excitation energies, first-order excited state properties, polarizabilities, first-hyperpolarizabilities, and two-photon absorptions strengths of formaldehyde suggests that DFT may in some cases be a sufficiently reliable alternative to high-level theory, such as coupled-cluster (CC) theory, in modeling solvent shifts, whereas results obtained with the HF wave function deviate significantly from the CC results. Calculations carried out on water gives results that also are comparable with CC calculations in accuracy for ground-state and first-order properties. However, to obtain such accuracy an exchange-correlation functional capable of describing the diffuse Rydberg states must be chosen.     

A molecular mechanics approach to mapping the conformational space of diaryl and triarylphosphines

A molecular mechanics force field has been developed which accurately reproduces experimental solid state structures and conformer interconversion barriers for a series of sterically congested diaryl and triaryl phosphines and some of their chalcogenide and Cr(CO)5 derivatives.     

Calculation of excited-state properties using general coupled-cluster and configuration-interaction models

Using string-based algorithms excitation energies and analytic first derivatives for excited states have been implemented for general coupled-cluster (CC) models within CC linear-response (LR) theory which is equivalent to the equation-of-motion (EOM) CC approach for these quantities. Transition moments between the ground and excited states are also considered in the framework of linear-response theory. The presented procedures are applicable to both single-reference-type and multireference-type CC wave functions independently of the excitation manifold constituting the cluster operator and the space in which the effective Hamiltonian is diagonalized. The performance of different LR-CC/EOM-CC and configuration-interaction approaches for excited states is compared. The effect of higher excitations on excited-state properties is demonstrated in benchmark calculations for NH(2) and NH(3). As a first application, the stationary points of the S(1) surface of acetylene are characterized by high-accuracy calculations.     

Nuclear spin-spin coupling constants in a coupled-cluster polarization propagator approach

A recently derived coupled-cluster doubles polarization propagator approximation (CCDPPA) for excitation energies and transition moments is extended to the calculation of nuclear spin-spin coupling constants. As expected, in cases where the perturbation is small (e.g. C₂H₂) the difference between results obtained using the present scheme and results obtained using the perturbative second-order polarization propagator approach (SOPPA) is small (1-5%). However, for CH⁺ the difference is found to be more than 40%.     

Integrating quantum and molecular mechanics

A computer algorithm is developed for integrating density functional quantum mechanics into a molecular mechanics program. The computationally infeasible aspects of the standard LCAO-MO approach (the iterative calculation of eigenvectors and the requirement of orthogonal expansions for the orbitals) are replaced with an efficient use of optimization via the trace theorem of linear algebra. The construction of a basis is also described for expanding the electron density that transforms with the molecular geometry. The combination of the trace method and the basis allow the solution for one configuration of atoms and electrons to be tracked over a wide range of internal conformations. The approach is readily adaptable to being used in the context of an imposed classical field that allows it to be used on part of a macromolecular complex. The initial implementation in the program AMMP is described. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 1618–1633, 1999     

Conformational properties and homolytic bond cleavage of organic peroxides. I. An empirical approach based upon molecular mechanics and ab initio calculations

The conformational features of a large number of hydroperoxides ROOH and peroxides ROOR′, where R and R′ are alkyl groups of different and increasing size and phenyl rings, including ortho substituted derivatives, were obtained from molecular mechanics calculations by employing a standard package. For the molecules of small molecular size, comparison was carried out with the results of ab initio calculations. Heats of formation were also obtained from molecular mechanics for hydroperoxides and peroxides: The values are, in general, overestimated. For the molecules containing the CF₃ group, the calculated values are subject to large errors and heats of formation were obtained from ab initio total energies in the “atom equivalents” scheme. To estimate the homolytic dissociation energies of the different bonds in the peroxide molecules, heats of formation of R·, ·OR, and ·OOR radicals were employed and several of them had to be calculated. Different approaches were employed—molecular mechanics calculations, ab initio energies within the atom equivalent and isodesmic reaction schemes, and Benson's group additivity rule; values consistent within the different calculation methods were chosen for estimating dissociation energies. The bond dissociation energies indicate different trends in these molecules as a function of the nature of the R and R′ groups and the possible electronic effects operating in these molecules are discussed. © 1993 John Wiley & Sons, Inc.     

Pyrrolizidine alkaloids necine bases: Ab initio,semiempirical, and molecular mechanics approaches to molecular properties

The structural stabilities of endo and exo conformations of retronecine and heliotridine molecules were analyzed using different ab initio, semiempirical, and molecular mechanics methods. All electron and pseudopotential ab initio calculations at the Hartree-Fock level of theory with 6-31G* and CEP-31G* basis sets provided structures in excellent agreement with available experimental results obtained from X-ray crystal structure and ¹H-NMR (nuclear magnetic resonance) studies in D₂O solutions. The exo conformations showed a greater stability for both molecules. The most significant difference between the calculations was found in the ring planarity of heliotridine, whose distortion was associated with the interaction between the O(11)H group and the C(1)-C(2) double bond as well as with a hydrogen bond between O(11)H and N(4). The discrepancy between pseudopotential and all-electron optimized geometries was reduced after inclusion of the innermost electrons of C(1), C(2), and N(4) in the core potential calculation. The MNDO, AM1, and PM3 semiempirical results showed poor agreement with experimental data. The five-membered rings were observed to be planar for AM1 and MNDO calculations. The PM3 calculations for exo-retronecine showed a greater stability than the endo conformer, in agreement with ab initio results. A good agreement was observed between MM3 and ab initio geometries, with small differences probably due to hydrogen bonds. While exo-retronecine was calculated to be more stable than the endo conformer, the MM3 calculations suggested that endo-heliotridine was slightly more stable than the exo form. © 1996 by John Wiley & Sons, Inc.     

New hybrid method for reactive systems from integrating molecular orbital or molecular mechanics methods with analytical potential energy surfaces

A computational approach to calculating potential energy surfaces for reactive systems is presented and tested. This hybrid approach is based on integrated methods where calculations for a small model system are performed by using analytical potential energy surfaces, and for the real system by using molecular orbital or molecular mechanics methods. The method is tested on a hydrogen abstraction reaction by using the variational transition-state theory with multidimensional tunneling corrections. The agreement between the calculated and experimental information depends on the quality of the method chosen for the real system. When the real system is treated by accurate quantum mechanics methods, the rate constants are in excellent agreement with the experimental measurements over a wide temperature range. When the real system is treated by molecular mechanics methods, the results are still good, which is very encouraging since molecular mechanics itself is not at all capable of describing this reactive system. Since no experimental information or additional fits are required to apply this method, it can be used to improve the accuracy of molecular orbital methods or to extend the molecular mechanics method to treat any reactive system with the single constraint of the availability of an analytical potential energy surface that describes the model system.     

A constrained variational approach for energy derivatives in Fock-space multireference coupled-cluster theory

In this paper, we present a formulation based on constrained variational approach to enable efficient computation of energy derivatives using Fock-space multireference coupled-cluster theory. Adopting conventional normal ordered exponential with Bloch projection approach, we present a method of deriving equations when general incomplete model spaces are used. Essential simplifications arise when effective Hamiltonian definition becomes explicit as in the case of complete model spaces or some special quasicomplete model spaces. We apply the method to derive explicit generic expressions upto third-order energy derivatives for [0,1], [1,0], and [1,1] Fock-space sectors. Specific diagrammatic expressions for zeroth-order Lagrange multiplier equations for [0,1], [1,0], and [1,1] sectors are presented.