QM/MM calculation of solvent effects on absorption spectra of guanine

Electronic spectra of guanine in the gas phase and in water were studied by quantum mechanical/molecular mechanical (QM/MM) methods. Geometries for the excited‐state calculations were extracted from ground‐state molecular dynamics (MD) simulations using the self‐consistent‐charge density functional tight binding (SCC‐DFTB) method for the QM region and the TIP3P force field for the water environment. Theoretical absorption spectra were generated from excitation energies and oscillator strengths calculated for 50 to 500 MD snapshots of guanine in the gas phase (QM) and in solution (QM/MM). The excited‐state calculations used time‐dependent density functional theory (TDDFT) and the DFT‐based multireference configuration interaction (DFT/MRCI) method of Grimme and Waletzke, in combination with two basis sets. Our investigation covered keto‐N7H and keto‐N9H guanine, with particular focus on solvent effects in the low‐energy spectrum of the keto‐N9H tautomer. When compared with the vertical excitation energies of gas‐phase guanine at the optimized DFT (B3LYP/TZVP) geometry, the maxima in the computed solution spectra are shifted by several tenths of an eV. Three effects contribute: the use of SCC‐DFTB‐based rather than B3LYP‐based geometries in the MD snapshots (red shift of ca. 0.1 eV), explicit inclusion of nuclear motion through the MD snapshots (red shift of ca. 0.1 eV), and intrinsic solvent effects (differences in the absorption maxima in the computed gas‐phase and solution spectra, typically ca. 0.1–0.3 eV). A detailed analysis of the results indicates that the intrinsic solvent effects arise both from solvent‐induced structural changes and from electrostatic solute–solvent interactions, the latter being dominant. © 2009 Wiley Periodicals, Inc. J Comput Chem 2010     

A flexible implementation of frozen-density embedding for use in multilevel simulations

A new implementation of frozen-density embedding (FDE) in the Amsterdam Density Functional (ADF) program package is presented. FDE is based on a subsystem formulation of density-functional theory (DFT), in which a large system is assembled from an arbitrary number of subsystems, which are coupled by an effective embedding potential. The new implementation allows both an optimization of all subsystems as a linear-scaling alternative to a conventional DFT treatment, the calculation of one active fragment in the presence of a frozen environment, and intermediate setups, in which individual subsystems are fully optimized, partially optimized, or completely frozen. It is shown how this flexible setup can facilitate the application of FDE in multilevel simulations.     

Quantum Mechanics/Molecular Mechanics Modeling of Enzymatic Processes: Caveats and Breakthroughs

Nature has developed large groups of enzymatic catalysts with the aim to transfer substrates into useful products, which enables biosystems to perform all their natural functions. As such, all biochemical processes in our body (we drink, we eat, we breath, we sleep, etc.) are governed by enzymes. One of the problems associated with research on biocatalysts is that they react so fast that details of their reaction mechanisms cannot be obtained with experimental work. In recent years, major advances in computational hardware and software have been made and now large (bio)chemical systems can be studied using accurate computational techniques. One such technique is the quantum mechanics/molecular mechanics (QM/MM) technique, which has gained major momentum in recent years. Unfortunately, it is not a black‐box method that is easily applied, but requires careful set‐up procedures. In this work we give an overview on the technical difficulties and caveats of QM/MM and discuss work‐protocols developed in our groups for running successful QM/MM calculations.     

Influence of the protein and DFT method on the broken‐symmetry and spin states in nitrogenase

The enzyme nitrogenase contains a complicated MoFe₇CS₉ cofactor with 35 possible broken‐symmetry (BS) states. We have studied how the energies of these states depend on the geometry, the surrounding protein, the DFT functional and the basis set, studying the resting state, a one‐electron reduced state and a protonated state. We find that the effect of the basis set is small, up to 11 kJ/mol. Likewise, the effect of the surrounding protein is restricted, up to 10 and 7 kJ/mol for the electrostatic and van der Waals energy terms. Single‐point energies calculated on a single geometry give a good correlation (R² = 0.92‐0.98) to energies calculated after geometry optimization, but some BS states may be disfavored by up to 37 kJ/mol. A change from the pure TPSS functional to the hybrid B3LYP functional may change the relative energies by up to 58 kJ/mol and the correlation between the two results is only 0.57‐0.72. Both functionals agree that BS7 is the most stable BS state and that the ground spin state is the quartet for the resting state and the quintet for the reduced state. With the TPSS functional, the BS6 state is the second most stable state, always at least 21 kJ/mol less stable than the BS7 state. However, with the B3LYP functional, BS10 is the second most stable state and for the protonated state it comes close in energy. Based on these results, we suggest a procedure how to consider the 35 BS states in future investigations of the nitrogenase reaction mechanism.     

DFT assessment of the spectroscopic constants and absorption spectra of neutral and charged diatomic species of group 11 and 14 elements

The spectroscopic constants and absorption spectra of neutral and charged diatomic molecules of group 11 and 14 elements formulated as [M₂]^+/0/? (M = Cu, Ag, Au), and [E₂]^+/0/? (E = C, Si, Ge, Sn, Pb) have been calculated at the PBE0/Def2‐QZVPP level of theory. The electronic and bonding properties of the diatomics have been analyzed by natural bond orbital analysis approach and topology analysis by the atoms in molecules method. Particular emphasis was given on the absorption spectra of the diatomic species, which were simulated by time‐dependent density functional theory calculations employing the hybrid Coulomb‐attenuating CAM‐B3LYP density functional. The simulated absorption spectra of the [M₂]^+/0/? (M = Cu, Ag, Au) and [E₂]^+/0/? (E = C, Si, Ge, Sn, Pb) species are in close resemblance with the experimentally observed spectra whenever available. The neutral M₂ and E₂ diatomics strongly absorb in the ultraviolet region, given rise to UVC, UVA and in a few cases UVB absorptions. In a few cases, weak absorbion bands also occur in the visible region. The absorption bands have thoroughly been analyzed and assignments of the contributing principal electronic transitions associated to individual excitations have been made. © 2014 Wiley Periodicals, Inc.     

The Role of Hydrogen Bonds and Electrostatic Interactions in Enhancing Two-Photon Absorption in Green and Yellow Fluorescent Proteins

The spectral properties of fluorescent proteins (FPs) depend on the protein environment of the chromophore (CRO). A deeper understanding of the CRO – environment interactions in terms of FPs’ spectral characteristics will allow for a rational design of novel markers with desired properties. Here, we are taking a step towards achieving this important goal. With the time-dependent density functional theory (TDDFT), we calculate one- and two-photon absorption (OPA and TPA) spectra for 5 green FPs (GFPs) and 3 yellow FPs (YFPs) differing in amino acid sequence. The goal is to reveal the roles of: (i) electrostatic interactions, (ii) hydrogen-bonds (h-bonds) and (iii) h-bonds together with distant electrostatic field in absorption spectra tuning. Our results point to design hypothesis towards FPs optimised for TPA-based applications. Both h-bonds and electrostatic interactions co-operate in enhancing TPA cross-section ( ) for the transition in GFPs. Furthermore, it seems that details of h-bonds network in the CRO's vicinity influences response to CRO – environment electrostatic interactions in YFPs. We postulate that engineering FPs with more hydrophilic CRO's environment can lead to greater . We also find that removing h-bonds formed with the CRO's phenolate leads to TPA enhancement for transition to higher excited states than S₁. Particularly Y145 and T203 residues are important in this regard.     

Steric Effects Govern the Photoactivation of Phytochromes

Phytochromes constitute a superfamily of photoreceptor proteins existing in two forms that absorb red (Pr) and far‐red (Pfr) light. Although it is well‐known that the conversion of Pr into Pfr (the biologically active form) is triggered by a Z→E photoisomerization of the linear tetrapyrrole chromophore, direct evidence is scarce as to why this reaction always occurs at the methine bridge between pyrrole rings C and D. Here, we present hybrid quantum mechanics/molecular mechanics calculations based on a high‐resolution Pr crystal structure of Deinococcus radiodurans bacteriophytochrome to investigate the competition between all possible photoisomerizations at the three different (AB, BC and CD) methine bridges. The results demonstrate that steric interactions with the protein are a key discriminator between the different reaction channels. In particular, it is found that such interactions render photoisomerizations at the AB and BC bridges much less probable than photoisomerization at the CD bridge.     

QM/MM vibrational mode tracking

Vibrational spectroscopy is a powerful tool to investigate the structure and dynamics of biomolecules. When small subsystems of large molecules such as active centers of enzymes are studied, quantum chemical calculations based on quantum mechanics/molecular mechanics (QM/MM) coupling schemes are a valuable means to interpret the spectra. The goal of this work is a methodological pilot study on how to selectively and thus efficiently extract certain vibrational information for extended molecular systems described by QM/MM methods. This is achieved by an extension of the mode tracking algorithm and a comparison with the partial Hessian diagonalization approach. After validating the methodology for the CO stretching vibration of 2-butanone and a delocalized CO stretch in acetylacetone, the stretching and bending modes of the CO ligand in CO myoglobin are tracked. Such systems represent an ideal application for mode tracking, because only a few strongly localized vibrations are sought for, while the large remainder of the molecule is of interest only as far as it affects these local vibrations. This influence is treated exactly by mode tracking.     

Isocyanide in Biochemistry? A Theoretical Investigation of the Electronic Effects and Energetics of Cyanide Ligand Protonation in [FeFe]‐Hydrogenases

The presence of Fe‐bound cyanide ligands in the active site of the proton‐reducing enzymes [FeFe]‐hydrogenases has led to the hypothesis that such Brønsted–Lowry bases could be protonated during the catalytic cycle, thus implying that hydrogen isocyanide (HNC) might have a relevant role in such crucial microbial metabolic paths. We present a hybrid quantum mechanical/molecular mechanical (QM/MM) study of the energetics of CN^? protonation in the enzyme, and of the effects that cyanide protonation can have on [FeFe]‐hydrogenase active sites. A detailed analysis of the electronic properties of the models and of the energy profile associated with H₂ evolution clearly shows that such protonation is dysfunctional for the catalytic process. However, the inclusion of the protein matrix surrounding the active site in our QM/MM models allowed us to demonstrate that the amino acid environment was finely selected through evolution, specifically to lower the Brønsted–Lowry basicity of the cyanide ligands. In fact, the conserved hydrogen‐bonding network formed by these ligands and the neighboring amino acid residues is able to impede CN^? protonation, as shown by the fact that the isocyanide forms of [FeFe]‐hydrogenases do not correspond to stationary points on the enzyme QM/MM potential‐energy surface.     

Computational mutation analysis of hydrogen abstraction and radical rearrangement steps in the catalysis of coenzyme B12-dependent diol dehydratase

A mutation analysis of the catalytic functions of active-site residues of coenzyme B(12)-dependent diol dehydratase in the conversion of 1,2-propanediol to 1,1-propanediol has been carried out by using QM/MM computations. Mutants His143Ala, Glu170Gln, Glu170Ala, and Glu170Ala/Glu221Ala were considered to estimate the impact of the mutations of His143 and Glu170. In the His143Ala mutant the activation energy for OH migration increased to 16.4 from 11.5 kcal mol(-1) in the wild-type enzyme. The highest activation energy, 19.6 kcal mol(-1), was measured for hydrogen back-abstraction in this reaction. The transition state for OH migration is not sufficiently stabilized by the hydrogen-bonding interaction formed between the spectator OH group and Gln170 in the Glu170Gln mutant, which demonstrates that a strong proton acceptor is required to promote OH migration. In the Glu170Ala mutant, a new strong hydrogen bond is formed between the spectator OH group and Glu221. A computed activation energy of 13.6 kcal mol(-1) for OH migration in the Glu170Ala mutant is only 2.1 kcal mol(-1) higher than the corresponding barrier in the wild-type enzyme. Despite the low activation barrier, the Glu170Ala mutant is inactive because the subsequent hydrogen back-abstraction is energetically demanding in this mutant. OH migration is not feasible in the Glu170Ala/Glu221Ala mutant because the activation barrier for OH migration is greatly increased by the loss of COO(-) groups near the spectator OH group. This result indicates that the effect of partial deprotonation of the spectator OH group is the most important factor in reducing the activation barrier for OH migration in the conversion of 1,2-propanediol to 1,1-propanediol catalyzed by diol dehydratase.     

Ab initio modeling of optical spectra in pH‐sensitive diarylethenes

The photochromic and acidochromic shifts undergone by recently synthesized diarylethene photochromes have been simulated using a Time‐Dependent Density Functional Theory approach relying on a range‐separated functional, namely CAM‐B3LYP. The selected approach is generally accurate for reproducing the variations of the spectral features, though acidochromic shifts are clearly more challenging than their photochromic counterparts. More importantly, an analyzis of the shapes of the relevant molecular orbitals grants insights into the electro‐cyclization of several diarylethenes, therefore partly allowing to understand the presence of experimental deadlocks. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

Extension of QM/MM docking and its applications to metalloproteins

To overcome the limitation of conventional docking methods which assume fixed charge model from force field parameters, combined quantum mechanics/molecular mechanics (QM/MM) method has been applied to docking as a variable charge model and shown to exhibit improvement on the docking accuracy over fixed charge based methods. However, it has also been shown that there are a number of examples for which adoption of variable‐charge model fails to reproduce the native binding modes. In particular, for metalloproteins, previously implemented method of QM/MM docking failed most often. This class of proteins has highly polarized binding sites at which high‐coordinate‐numbered metal ions reside. We extend the QM/MM docking method so that protein atoms surrounding the binding site along with metal ions are included as quantum region, as opposed to only ligand atoms. This extension facilitates the required scaling of partial charges on metal ions leading to prediction of correct binding modes in metalloproteins. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009     

Role of doping and sheet size in tailoring optoelectronic properties of germanene: A TDDFT study

Germanene is a novel 2D material with promising optoelectronic properties, tuning of which is to be explored. This work demonstrates that doping and increasing the sheet size can alter optical and electronic properties of germanene via perturbation of the band structure. This feature has also been observed in other nanostructures, notably, silicon nanostructures, and may be attributed to quantum confinement effects. Our main findings on H‐terminated germanene are, (i) band gap can be reduced by 30%, (ii) exciton binding energy can be reduced by 60%, and (iii) absorption spectra can be tuned from UV to visible range. We employ time‐dependent density functional theory to investigate the role of dopants, boron (B), phosphorus (P), carbon (C), silicon (Si), and zirconium (Zr). Width of the germanene sheet is varied from 0.78 nm to 2.78 nm. Frequency and energy calculations are carried out to analyze the infrared (IR) and ultra‐violet (UV)‐visible (VIS) spectra.     

A multiscale study on photophysical properties of a novel fluorescent probe for imaging amyloid-β in Alzheimer's disease

Detection of amyloid-β deposition in the brain region is of significant importance for early diagnosis of Alzheimer's disease (AD). In the last few decades, the fluorescent imaging technique has been considered an effective tool for detecting amyloid-β plaques due to its safety, sensitivity, and operability. Thus, numerous fluorescent probes for amyloid-β have been developed. The design of a probe with high selectivity and improved sensing performance requires knowledge about the potential binding sites for the probe in amyloid-β and local microstructure of the probe in different sites. In this study, amyloid-β-specific photophysical properties of a novel fluorescent probe (cis-PAD-1) are theoretically investigated by using multiscale simulations, including molecular docking and quantum mechanics/molecular mechanics calculations. Binding profile of cis-PAD-1 in amyloid-β has been simulated, and binding affinity of the probe in various sites is calculated. An excited-state property study on cis-PAD-1 illustrates that the probe shows remarkable fluorescence enhancement in amyloid-β due to the influence of the microenvironment, which is consistent with the experimental observation. Most importantly, two-photon absorption cross section of the probe is greatly increased in the near-infrared region when targeting with amyloid-β owing to the enhanced transition dipole moment. Therefore, one can propose the usage of cis-PAD-1 as an excellent candidate in two-photon fluorescent imaging for amyloid-β. The detailed investigations provide information on the development and design strategy of a new fluorescent probe for amyloid-β imaging in AD.     

Contributions of pauli repulsions to the energetics and physical properties computed in QM/MM methods

Conventional combined quantum mechanical/molecular mechanical (QM/MM) methods lack explicit treatment of Pauli repulsions between the quantum‐mechanical and molecular‐mechanical subsystems. Instead, classical Lennard‐Jones (LJ) potentials between QM and MM nuclei are used to model electronic Pauli repulsion and long‐range London dispersion, despite the fact that the latter two are inherently of quantum nature. Use of the simple LJ potential in QM/MM methods can reproduce minimal geometries and energies of many molecular clusters reasonably well, as compared to full QM calculations. However, we show here that the LJ potential cannot correctly describe subtle details of the electron density of the QM subsystem because of the neglect of Pauli repulsions between the QM and MM subsystems. The inaccurate electron density subsequently affects the calculation of electronic and magnetic properties of the QM subsystem. To explicitly consider Pauli interactions with QM/MM methods, we propose a method to use empirical effective potentials on the MM atoms. The test case of the binding energy and magnetic properties of a water dimer shows promising results for the general application of effective potentials to mimic Pauli repulsions in QM/MM calculations. © 2013 Wiley Periodicals, Inc.     

Analytical excited state forces for the time-dependent density-functional tight-binding method

An analytical formulation for the geometrical derivatives of excitation energies within the time-dependent density-functional tight-binding (TD-DFTB) method is presented. The derivation is based on the auxiliary functional approach proposed in [Furche and Ahlrichs, J Chem Phys 2002, 117, 7433]. To validate the quality of the potential energy surfaces provided by the method, adiabatic excitation energies, excited state geometries, and harmonic vibrational frequencies were calculated for a test set of molecules in excited states of different symmetry and multiplicity. According to the results, the TD-DFTB scheme surpasses the performance of configuration interaction singles and the random phase approximation but has a lower quality than ab initio time-dependent density-functional theory. As a consequence of the special form of the approximations made in TD-DFTB, the scaling exponent of the method can be reduced to three, similar to the ground state. The low scaling prefactor and the satisfactory accuracy of the method makes TD-DFTB especially suitable for molecular dynamics simulations of dozens of atoms as well as for the computation of luminescence spectra of systems containing hundreds of atoms.     

Quantum mechanical study on plasmon resonances in small ring clusters

The collectivity of the electronic motion in small sodium clusters with ring structure is studied by time‐dependent density functional theory. The formation and development of collective resonances in the absorption spectra were obtained as a function of the ring radius. In small ring clusters, besides the lower‐energy mode and the higher‐energy mode, there is another plasmon resonance mode, that is, the reverse two‐dipole mode. For the reverse two‐dipole mode, the formations of these two dipoles are due to the external field inducement and the shielding effect, although the resonant excitation is mainly due to the coupling effect of the electrons of these two dipoles. © 2012 Wiley Periodicals, Inc.