Calculations on the electronic excited states of ureas and oligoureas

We report CASPT2 calculations on the electronic excited states of several ureas. For monoureas, we find an electric dipole forbidden n --> pi* transition between 180 and 210 nm, dependent on the geometry and substituents of the urea. We find two intense pinb --> pi* transitions between 150 and 210 nm, which account for the absorptions seen in the experimental spectra. The n' --> pi* and pib --> pi* transitions are at wavelengths below 125 nm, which is below the lower limit of the experimental spectra. Parameter sets modeling the charge densities of the electronic transitions have been derived and permit calculations on larger oligoureas, using the exciton matrix method. For glycouril, a urea dimer, both the CASPT2 method and the matrix method yield similar results. Calculations of the electronic circular dichroism spectrum of an oligourea containing eight urea groups indicate that the experimental spectrum cannot be reproduced without the inclusion of electronic excitations involving the side chains. These calculations are one of the first attempts to understand the relationship between the structure and excited states of this class of macromolecule.     

Potential energy landscape of the photoinduced multiple proton-transfer process in the green fluorescent protein: classical molecular dynamics and multiconfigurational electronic structure calculations

The green fluorescent protein proton wire operating upon photoexcitation of the internally caged chromophore is investigated by means of classical molecular dynamics and multiconfigurational electronic structure calculations. The structure of the proton wire is studied for the solvated protein, showing that the wire is likely to be found in a configuration ready to operate as soon as the chromophore is photoexcited, and leading to a total of three proton translocations in the vicinity of the chromophore. Multiconfigurational CASSCF and CASPT2 calculations provide a detailed overview of the energy landscape of the proton wire for the ground electronic state S0, the photoactive 1pi pi* state, and the charge-transfer 1pi sigma* state. The results allow discussion of the operation of the wire in terms of the sequence of proton-transfer events and the participation of each electronic state.     

Thermal and solvent effects on the NMR and UV parameters of some bioreductive drugs

15N NMR chemical shifts and n-->pi* electronic transition energy for metronidazole (1) has been calculated and compared with experimental data. A detailed computational study of 1 is presented, with special attention to the performance of various theoretical methods for reproducing spectroscopic parameters in solution. The most sophisticated approach involves density functional based on the Car-Parrinello molecular dynamics simulations of 1 in aqueous solution (BP86 level) and averaging chemical shifts and deltaE(n-->pi*) over snapshots from the trajectory. In the NMR and UV calculations for these snapshots (performed at the B3LYP level), a small number of discrete water molecules are retained, and the remaining bulk solution effects are included via a polarizable continuum model (PCM). A good agreement with experiment is also obtained using static geometry optimization and NMR computation of pristine 1 employing a PCM approach. Further theoretical predictions are also reported for 17O NMR and deltaE(n-->pi*) of three hydroxycinnamic acid derivatives, which suggest that it is essential to incorporate the dynamics and solvent effects for NMR and UV calculations in the condensed phase.     

A sequential molecular mechanics/quantum mechanics study of the electronic spectra of amides

We report gas-phase electronic spectra of formamide, N-methyformamide, acetamide, and N-methylacetamide at 300 K calculated using a combination of classical molecular dynamics and time-dependent density functional theory (TDDFT). In comparison to excitation energies computed using the global minima structures, the valence npi* and pi(nb)pi* states show a significant red-shift of 0.1-0.35 eV, while smaller shifts are found for the n3s and pi(nb)3s Rydberg states. In this work, we have identified the physical origin of these shifts arising from variations of the molecular structure. We present simple relationships between key geometrical parameters and spectral shifts. Consequently, electronic spectra can be generated directly from ground-state structures, without additional quantum chemical calculations. The electronic spectrum of formamide in aqueous solution is computed using TDDFT using an explicit solvent model. This provides a quantitative determination of the condensed-phase spectrum. In general, this study shows that temperature effects can change the predicted excitation energies significantly and demonstrates how electronic spectra at elevated temperatures can be computed in a computationally efficient way.     

High-resolution inner-shell excitation spectroscopy of H2-phthalocyanine

We report on a combined experimental and theoretical carbon and nitrogen K-edge near-edge x-ray absorption fine structure investigation on condensed metal-free phthalocyanine (H2Pc). Based on the results from improved virtual orbital calculations, all resonances in the experimental high-resolution data can be assigned to various electronic transitions. The comparison between experiments and calculations further shows that a significant influence of the core hole, which affects both the transition energies and the cross sections, is present and must be considered in theoretical approaches. Moreover, additional fine structure is clearly resolved for the first N 1s-->pi* transition, which can be interpreted as vibronic coupling to the electronic core excitation.     

The Gaussian and augmented-plane-wave density functional method for ab initio molecular dynamics simulations

A new algorithm for density-functional-theory-based ab initio molecular dynamics simulations is presented. The Kohn–Sham orbitals are expanded in Gaussian-type functions and an augmented-plane-wave-type approach is used to represent the electronic density. This extends previous work of ours where the density was expanded only in plane waves. We describe the total density in a smooth extended part which we represent in plane waves as in our previous work and parts localised close to the nuclei which are expanded in Gaussians. Using this representation of the charge we show how the localised and extended part can be treated separately, achieving a computational cost for the calculation of the Kohn–Sham matrix that scales with the system size N as O(NlogN). Furthermore, we are able to reduce drastically the size of the plane-wave basis. In addition, we introduce a multiple-cutoff method that improves considerably the performance of this approach. Finally, we demonstrate with a series of numerical examples the accuracy and efficiency of the new algorithm, both for electronic structure calculations and for ab initio molecular dynamics simulations. Received: 15 December 1998 /Accepted: 18 February 1999 /Published online: 14 July 1999     

Electronic structure and spectra of catechol and alizarin in the gas phase and attached to titanium

Ab initio electronic structure calculations elucidate the dramatic differences observed in the electronic spectra of the catechol and alizarin molecules upon binding to titanium. Catechol and alizarin are similar chromophores with analogous electronic spectra in the free state. Binding alizarin to titanium red-shifts the spectrum. The binding of catechol to titanium produces a new optically active transition, at the same time preserving the features of the free catechol spectrum. By examining the details of the calculations, we can rationalize the spectral differences in the catechol and alizarin systems by the positioning of the catechol and alizarin pi molecular orbitals relative to the conduction band of TiO(2).     

Expansion of linear combinations of slater-type orbitals in eigenfunctions of the three-dimensional isotropic harmonic oscillator

Several classes of functions related to the Gaussian have been used with success as basis sets for the representation of atomic and molecular orbitals. We have compared the representation of a hydrogen 1s orbital by a sum of Gaussian lobe functions with its expansion in eigenfunctions of the three-dimensional isotropic harmonic oscillator. The lobe functions are shown to achieve better expectation values of the energy, with fewer terms. The lobe functions have the further computational advantage of not containing high powers of the radius. It is concluded that the lobe functions are a superior basis set for use in calculations of the electronic structure of atoms and molecules.     

Influence of Intermolecular Vibrations on the Electronic Coupling in Organic Semiconductors: The Case of Anthracene and Perfluoropentacene

We have performed classical molecular dynamics simulations and quantum‐chemical calculations on molecular crystals of anthracene and perfluoropentacene. Our goal is to characterize the amplitudes of the room‐temperature molecular displacements and the corresponding thermal fluctuations in electronic transfer integrals, which constitute a key parameter for charge transport in organic semiconductors. Our calculations show that the thermal fluctuations lead to Gaussian‐like distributions of the transfer integrals centered around the values obtained for the equilibrium crystal geometry. The calculated distributions have been plugged into Monte‐Carlo simulations of hopping transport, which show that lattice vibrations impact charge transport properties to various degrees depending on the actual crystal structure.     

Calculations of molecules,clusters, and solids with a simplified LCAO-DFT-LDA scheme

A simplified LCAO-DFT-LDA scheme for calculations of structure and electronic structure of large molecules, clusters, and solids is presented. Forces on the atoms are calculated in a semiempirical way considering the electronic states. The small computational effort of this treatment allows one to perform molecular dynamics (MD ) simulations of molecules and clusters up to a few hundred atoms as well as corresponding simulations of condensed systems within the Born-Oppenheimer approximation. The accuracy of the method is illustrated by the results of calculations for a series of small molecules and clusters. © 1996 John Wiley & Sons, Inc.     

Testing computational models of hyperpolarizability in a merocyanine dye using spectroscopic and DFT methods

The structural and electronic properties of a highly solvatochromic merocyanine dye, 2-(3-cyano-5,5-dimethyl-4-(3-(1-octadecylpyridin-4(1H)-ylidene)prop-1-enyl)furan-2(5H)-ylidene)malononitrile (pyr3pi), have been investigated using UV-vis, NMR, hyper-Rayleigh scattering, and Raman spectroscopies and further interpreted using computational chemistry. Spectroscopic data indicate that pyr3pi exists in its zwitterionic form even in low polarity solvents with electronic absorption spectra showing a hypsochromic shift with an increase in solvent polarity and NMR experiments indicating an increasingly zwitterionic structure in chloroform as the temperature is lowered. Raman spectra in increasingly polar solvents show small variations of the structure that are consistent with a change toward a structure with more zwitterionic character. However, comparison of the calculated and experimental vibrational energies and intensities and comparison of NMR coupling constants with calculated bond order indicate that calculations underestimate the amount of charge separation seen in low polarity solvents. Although for this system density functional theory (DFT) calculations and the two-state model qualitatively reproduce negative solvatochromism, they fail to reproduce the trends in hyperpolarizability seen experimentally. This is attributed to solvent field DFT calculations underestimating the degree of charge separation in reaction fields representing low polarity solvents.     

Semiempirical implementation of strictly localized geminals for analysis of molecular electronic structure

Approximate electronic trial wave function taken as the antisymmetrized product of strictly localized geminals (APSLG) is implemented for semiempirical analysis of molecular electronic structure of “organic” compounds and for calculations of their heats of formation. This resulted in an O(N)‐scaling method. Using the MINDO/3 form of the semiempirical Hamiltonian with reparameterized β_AB values in combination with the APSLG form of the wave function yields the computational procedure BF'98. Calculations on the heats formation and the equilibrium geometries for a wide range of molecules show that the APSLG‐MINDO/3 approach is more favorable than its self‐consistent field‐based counterpart. Also, the APSLG formalism allows to interpret molecular electronic wave function in chemically sensible terms. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 752–764, 2001     

Stereoelectronic effects on molecular geometries and state-energy splittings of ligated monocopper dioxygen complexes

The relative energies of side-on versus end-on binding of molecular oxygen to a supported Cu(I) species, and the singlet versus triplet nature of the ground electronic state, are sensitive to the nature of the supporting ligands and, in particular, depend upon their geometric arrangement relative to the O2 binding site. Highly correlated ab initio and density functional theory electronic structure calculations demonstrate that optimal overlap (and oxidative charge transfer) occurs for the side-on geometry, and this is promoted by ligands that raise the energy, thereby enhancing resonance, of the filled Cu dxz orbital that hybridizes with the in-plane pi* orbital of O2. Conversely, ligands that raise the energy of the filled Cu dz2 orbital foster a preference for end-on binding as this is the only mode that permits good overlap with the in-plane O2 pi*. Because the overlap of Cu dz2 with O2 pi* is reduced as compared to the overlap of Cu dxz with the same O2 orbital, the resonance is also reduced, leading to generally more stable triplet states relative to singlets in the end-on geometry as compared to the side-on geometry, where singlet ground states become more easily accessible once ligands are stronger donors. Biradical Cu(II)-O2 superoxide character in the electronic structure of the supported complexes leads to significant challenges for accurate quantum chemical calculations that are best addressed by exploiting the spin-purified M06L local density functional, single-reference completely renormalized coupled-cluster theory, or multireference second-order perturbation theory, all of which provide predictions that are qualitatively and quantitatively consistent with one another.     

The weak hydrogen bond in the fluorobenzene-ammonia van der Waals complex: Insights into the effects of electron withdrawing substituents on pi versus in-plane bonding

The fluorobenzene-ammonia van der Waals complex has been studied using a combination of two-color resonance enhanced multiphoton ionization (REMPI) spectroscopy, counterpoise corrected RICC2 ab initio molecular orbital calculations, and multidimensional Franck-Condon analysis. The experimental REMPI spectrum is characterized by a dominant, blueshifted band origin, and weak activity in intermolecular vibrational modes. RICC2 geometry optimizations and numerical vibrational frequency calculations of the neutral ground and first excited states have been performed on a number of different structural isomers of the complex using basis sets ranging from augmented double-zeta to quadruple-zeta level. Ground state basis set superposition error corrected zero-point binding energies show the in-plane sigma complex, forming a pseudo-six-membered ring connecting the fluorine atom and ortho-hydrogen, to be consistently the most stable of all six conformations considered, at all levels of theory. Comparison of computed zero-point excitation energies for the most stable pi and sigma conformers with fluorobenzene show that the sigma complex is the only conformer predicted to exhibit a spectral blueshift upon electronic excitation. The computed neutral ground and first excited state geometries and frequencies were used to perform multidimensional Franck-Condon simulations of the S(1)-S(0) vibronic spectrum for each of the most stable conformers. These simulations yielded null spectra for transitions involving the most stable of the pi complexes, pi(bridge); a spectrum rich in strong intermolecular vibrational structure for the second of the pi complexes, in complete contrast to the experimental spectrum; and for the sigma complex, a spectrum exhibiting weak intermolecular activity in line with that observed experimentally. This last simulation allowed an almost complete vibrational assignment of the intermolecular structure in the REMPI spectrum. The agreement between computational results and experiment overwhelmingly favors assignment of the spectrum to the in-plane sigma complex.     

QM/MM modeling of compound I active species in cytochrome P450, cytochrome C peroxidase, and ascorbate peroxidase

QM/MM calculations provide a means for predicting the electronic structure of the metal center in metalloproteins. Two heme peroxidases, Cytochrome c Peroxidase (CcP) and Ascorbate Peroxidase (APX), have a structurally very similar active site, yet have active intermediates with very different electronic structures. We review our recent QM/MM calculations on these systems, and present new computational data. Our results are in good agreement with experiment, and suggest that the difference in electronic structure is due to a large number of small differences in structure from one protein to another. We also discuss recent QM/MM calculations on the active species of cytochrome P450, in which a similar sensitivity of the electronic structure to the environment is found. However, this does not appear to explain different catalytic profiles of the different drug-metabolizing isoforms of this class of enzyme.     

Deprotonation‐Induced Aromaticity Enhancement and New Conjugated Networks in meso‐Hexakis(pentafluorophenyl)[26]hexaphyrin

meso‐Hexakis(pentafluorophenyl)‐substituted neutral hexaphyrin with a 26π‐electronic circuit can be regarded as a real homolog of porphyrin with an 18π‐electronic circuit with respect to a quite flat molecular structure and strong aromaticity. We have investigated additional aromaticity enhancement of meso‐hexakis(pentafluorophenyl)[26]hexaphyrin(1.1.1.1.1.1) by deprotonation of the inner N? H groups in the macrocyclic molecular cavity to try to induce further structural planarization. Deprotonated mono‐ and dianions of [26]hexaphyrin display sharp B‐like bands, remarkably strong fluorescence, and long‐lived singlet and triplet excited‐states, which indicate enhanced aromaticity. Structural, spectroscopic, and computational studies have revealed that deprotonation induces structural deformations, which lead to a change in the main conjugated π‐electronic circuit and cause enhanced aromaticity.     

Natural bond orbital analysis in the ONETEP code: Applications to large protein systems

First principles electronic structure calculations are typically performed in terms of molecular orbitals (or bands), providing a straightforward theoretical avenue for approximations of increasing sophistication, but do not usually provide any qualitative chemical information about the system. We can derive such information via post‐processing using natural bond orbital (NBO) analysis, which produces a chemical picture of bonding in terms of localized Lewis‐type bond and lone pair orbitals that we can use to understand molecular structure and interactions. We present NBO analysis of large‐scale calculations with the ONETEP linear‐scaling density functional theory package, which we have interfaced with the NBO 5 analysis program. In ONETEP calculations involving thousands of atoms, one is typically interested in particular regions of a nanosystem whilst accounting for long‐range electronic effects from the entire system. We show that by transforming the Non‐orthogonal Generalized Wannier Functions of ONETEP to natural atomic orbitals, NBO analysis can be performed within a localized region in such a way that ensures the results are identical to an analysis on the full system. We demonstrate the capabilities of this approach by performing illustrative studies of large proteins—namely, investigating changes in charge transfer between the heme group of myoglobin and its ligands with increasing system size and between a protein and its explicit solvent, estimating the contribution of electronic delocalization to the stabilization of hydrogen bonds in the binding pocket of a drug‐receptor complex, and observing, in situ, the n → π* hyperconjugative interactions between carbonyl groups that stabilize protein backbones. © 2012 Wiley Periodicals, Inc.