Dmytro Kosenkov

Solvent effects on the electronic transitions of p-nitroaniline: a QM/EFP study.

Solvatochromic shifts of the electronic states of a chromophore can be used as a measure of solute-solvent interactions. The shifts of the electronic states of a model organic chromophore, p-nitroaniline (pNA), embedded in solvents with different polarities (water, 1,4-dioxane, and cyclohexane) are studied using a hybrid quantum mechanics/molecular-mechanics-type technique in which the chromophore is described by the configuration interaction singles with perturbative doubles (CIS(D)) method while the solvent is treated by the effective fragment potential (EFP) method. This newly developed CIS(D)/EFP scheme includes the quantum-mechanical coupling of the Coulomb and polarization terms; however, short-range dispersion and exchange-repulsion terms of EFP are not included in the quantum Hamiltonian. The CIS(D)/EFP model is benchmarked against the more accurate equation of motion coupled cluster with singles and doubles (EOM-CCSD)/EFP method on a set of small pNA-water clusters. CIS(D)/EFP accurately predicts the red solvatochromic shift of the charge-transfer π → π* state of pNA in polar water. The shift is underestimated in less polar dioxane and cyclohexane probably because of the omission of the explicit quantum-mechanical treatment of the short-range terms. Different solvation of singlet and triplet states of pNA results in different probabilities of intersystem crossing (ISC) and internal conversion (IC) pathways of energy relaxation in solvents of different polarity. Computed singlet-triplet splittings in water and dioxane qualitatively explain the active ISC channel in dioxane and predict almost no conversion to the triplet manifold in water, in agreement with experimental findings.

Accurate Prediction of Noncovalent Interaction Energies with the Effective Fragment Potential Method: Comparison of Energy Components to Symmetry-Adapted Perturbation Theory for the S22 Test Set

Noncovalent interactions play an important role in the stabilization of biological molecules. The effective fragment potential (EFP) is a computationally inexpensive ab initio-based method for modeling intermolecular interactions in noncovalently bound systems. The accuracy of EFP is benchmarked against the S22 and S66 data sets for noncovalent interactions [Jurečka, P.; Šponer, J.; Černý, J.; Hobza, P. Phys. Chem. Chem. Phys.2006, 8, 1985; Řezáč, J.; Riley, K. E.; Hobza, P. J. Chem. Theory Comput.2011, 7, 2427]. The mean unsigned error (MUE) of EFP interaction energies with respect to coupled-cluster singles, doubles, and perturbative triples in the complete basis set limit [CCSD(T)/CBS] is 0.9 and 0.6 kcal/mol for S22 and S66, respectively, which is similar to the MUE of MP2 and SCS-MP2 for the same data sets, but with a greatly reduced computational expense. Moreover, EFP outperforms classical force fields and popular DFT functionals such as B3LYP and PBE, while newer dispersion-corrected functionals provide a more accurate description of noncovalent interactions. Comparison of EFP energy components with the symmetry-adapted perturbation theory (SAPT) energies for the S22 data set shows that the main source of errors in EFP comes from Coulomb and polarization terms and provides a valuable benchmark for further improvements in the accuracy of EFP and force fields in general.

Noncovalent Interactions in Extended Systems Described by the Effective Fragment Potential Method: Theory and Application to Nucleobase Oligomers

The implementation of the effective fragment potential (EFP) method within the Q-CHEM electronic structure package is presented. The EFP method is used to study noncovalent π-π and hydrogen-bonding interactions in DNA strands. Since EFP is a computationally inexpensive alternative to high-level ab initio calculations, it is possible to go beyond the dimers of nucleic acid bases and to investigate the asymptotic behavior of different components of the total interaction energy. The calculations demonstrated that the dispersion energy is a leading component in π-stacked oligomers of all sizes. Exchange-repulsion energy also plays an important role. The contribution of polarization is small in these systems, whereas the magnitude of electrostatics varies. Pairwise fragment interactions (i.e., the sum of dimer binding energies) were found to be a good approximation for the oligomer energy.

Ab Initio Kinetic Simulation of Gas-Phase Experiments: Tautomerization of Cytosine and Guanine

A novel kinetic approach based on ab initio calculated rate constants has been developed and implemented in the kTSim program. The proposed approach allows prediction of the distribution of reactant and product concentrations over time, based exclusively on computationally obtained rate constants. The newly developed methodology was used to simulate the process of evaporation and tautomerization of guanine and cytosine under thermal (T = 490 K, cytosine; T = 620 K, guanine) and laser (T = 1000 K, 24 ns laser pulse) desorption conditions. Both monomolecular and bimolecular mechanisms of the tautomerization were considered simultaneously. The rates of the reactions were estimated using the values of Gibbs free energies calculated at the MPWB1K/aug-cc-pVDZ level and specified in a kTSim input. We expect that the proposed approach can also be used for accurate kinetic simulation of a wide range of processes.

Evolution of Amide Stacking in Larger γ-Peptides: Triamide H-Bonded Cycles

The single-conformation spectroscopy of two model γ-peptides has been studied under jet-cooled conditions in the gas phase. The methyl-capped triamides, Ac-γ(2)-hPhe-γ(2)-hAla-NHMe and Ac-γ(2)-hAla-γ(2)-hPhe-NHMe, were probed by resonant two-photon ionization (R2PI) and resonant ion-dip infrared (RIDIR) spectroscopies. Four conformers of Ac-γ(2)-hPhe-γ(2)-hAla-NHMe and three of Ac-γ(2)-hAla-γ(2)-hPhe-NHMe were observed and spectroscopically interrogated. On the basis of comparison with the predictions of density functional theory calculations employing a dispersion-corrected functional (ωB97X-D/6-311++G(d,p)), all seven conformers have been assigned to particular conformational families. The preference for formation of nine-membered rings (C9) observed in a previous study [James, W. H., III et al., J. Am. Chem. Soc. 2009, 131, 14243] of the smaller analog, Ac-γ(2)-hPhe-NHMe, carries over to these triamides, with four of the seven conformers forming C9/C9 sequential double-ring structures, and one conformer a C9/C14 bifurcated double ring. The remaining two conformers form C7/C7/C14 H-bonded cycles involving all three amide NH groups, unprecedented in other peptides and peptidomimetics. The amide groups in these structures form a H-bonded triangle with the two trimethylene bridges forming loops above and below the molecules midsection. The structure is a natural extension of amide stacking, with the two terminal amides blocked from forming the amide tristack by formation of the C14 H-bond. Pair interaction energy decomposition analysis based on the fragment molecular orbital method (FMO-PIEDA) is used to determine the nonbonded contributions to the stabilization of these conformers. Natural bond orbital (NBO) analysis identifies amide stacking with a pair of n → π* interactions between the nitrogen lone pairs and π* orbitals on the carbonyl of the opposing amide groups.

Effective fragment potential method in Q‐CHEM: A guide for users and developers

A detailed description of the implementation of the effective fragment potential (EFP) method in the Q‐CHEM electronic structure package is presented. The Q‐CHEM implementation interfaces EFP with standard quantum mechanical (QM) methods such as Hartree–Fock, density functional theory, perturbation theory, and coupled‐cluster methods, as well as with methods for electronically excited and open‐shell species, for example, configuration interaction, time‐dependent density functional theory, and equation‐of‐motion coupled‐cluster models. In addition to the QM/EFP functionality, a “fragment‐only” feature is also available (when the system is described by effective fragments only). To aid further developments of the EFP methodology, a detailed description of the C++ classes and EFP modules workflow is presented. The EFP input structure and EFP job options are described. To assist setting up and performing EFP calculations, a collection of Perl service scripts is provided. The precomputed EFP parameters for standard fragments such as common solvents are stored in Q‐CHEMs auxiliary library; they can be easily invoked, similar to specifying standard basis sets. The instructions for generating user‐defined EFP parameters are given. Fragments positions can be specified by their center of mass coordinates and Euler angles. The interface with the IQMOL and WEBMO software is also described.

Extension of the Effective Fragment Potential Method to Macromolecules

The effective fragment potential (EFP) approach, which can be described as a nonempirical polarizable force field, affords an accurate first-principles treatment of noncovalent interactions in extended systems. EFP can also describe the effect of the environment on the electronic properties (e.g., electronic excitation energies and ionization and electron-attachment energies) of a subsystem via the QM/EFP (quantum mechanics/EFP) polarizable embedding scheme. The original formulation of the method assumes that the system can be separated, without breaking covalent bonds, into closed-shell fragments, such as solvent and solute molecules. Here, we present an extension of the EFP method to macromolecules (mEFP). Several schemes for breaking a large molecule into small fragments described by EFP are presented and benchmarked. We focus on the electronic properties of molecules embedded into a protein environment and consider ionization, electron-attachment, and excitation energies (single-point calculations only). The model systems include chromophores of green and red fluorescent proteins surrounded by several nearby amino acid residues and phenolate bound to the T4 lysozyme. All mEFP schemes show robust performance and accurately reproduce the reference full QM calculations. For further applications of mEFP, we recommend either the scheme in which the peptide is cut along the Cα-C bond, giving rise to one fragment per amino acid, or the scheme with two cuts per amino acid, along the Cα-C and Cα-N bonds. While using these fragmentation schemes, the errors in solvatochromic shifts in electronic energy differences (excitation, ionization, electron detachment, or electron-attachment) do not exceed 0.1 eV. The largest error of QM/mEFP against QM/EFP (no fragmentation of the EFP part) is 0.06 eV (in most cases, the errors are 0.01-0.02 eV). The errors in the QM/molecular mechanics calculations with standard point charges can be as large as 0.3 eV.

Thermodynamics of Binding of Di- and Tetrasubstituted Naphthalene Diimide Ligands to DNA G-Quadruplex

Naphthalene diimide ligands have the potential to stabilize human telomeric G-quadruplex DNA via noncovalent interactions. Stabilization of G-quadruplex high order structures has become an important strategy to develop novel anticancer therapeutics. In this study four naphthalene diimide based ligands were analyzed in order to elucidate the principal factors determining contributions to G-quadruplex-ligand binding. Three possible modes of binding and their respective Gibbs free energies for two naphthalene diimide based di-N-alkylpyridinium substituted ligands have been determined using a molecular docking technique and compared to experimental results. The structures obtained from the molecular docking calculations, were analyzed using the ab initio based fragment molecular orbital (FMO) method in order to determine the major enthalpic contributions to the binding and types of interactions between the ligand and specific residues of the G-quadruplex. A computational methodology for the efficient and inexpensive ligand optimization as compared to fully ab initio methods based on the estimation of binding affinities of the naphthalene diimide derived ligands to G-quadruplex is proposed.

Thermodynamics and Kinetics of Intramolecular Water Assisted Proton Transfer in Na+-1-Methylcytosine Water Complexes

High-level ab initio predictions of the tautomerization equilibrium and rate constants of water-assisted proton transfer of 1-methyl-cytosine (MeC) to its MeC* imino tautomeric form in the presence of up to two water molecules (W) and the Na(+) cation were carried out. The calculated energy values were used to obtain the thermodynamic parameters and equilibrium concentration of MeC, its rare tautomer, and their complexes with up to two water molecules and the Na (+) cation. The rate constants for the tautomerization were obtained by using the instanton approach (a quasiclassical method based on the least-action principle). Hydration of MeC by one water molecule leads to an increase of the concentration of the MeC* tautomer in the equilibrium mixture and a decrease of the barrier of the MeC* formation (to 15.6 kcal/mol). If the Na(+) cation is present, the tautomeric form is much less favored, and the tautomerization barrier increases to 25.2 kcal/mol. It was found that MeC monohydrate has both the highest equilibrium (2.9 x 10(-2)) and rate (7.9 x 10(5) s(-1)) constants of tautomerization in comparison to the MeC*NaW and MeC*Na2W complexes containing the Na(+) cation. Moreover, this study also allows one to estimate the concentration of MeC present in the cell during DNA synthesis as the unwanted tautomer, which in forming a mismatched base pair can cause spontaneous point mutations. Kinetic simulations have demonstrated that the low values of equilibrium (10(-14)-10(-13)) and rate constants (10(-17)-10(-16) s(-1)) of tautomerization make contribution of the MeC*Na(+)W and MeC*Na(+)2W complexes to the point mutations in DNA unlikely. In contrast to these Na(+) complexes, MeC*W can reach an equilibrium concentration of 2.9 x 10(-2) within 10(-7) s; thus, it can increase the probability of the point mutations.

PyFREC: Software for Förster electronic coupling evaluation in molecular fragments

Electronic couplings are crucial for understanding exciton dynamics and associated energy transfer in artificial and natural chromophores. The proposed PyFREC (Python FRagment Electronic Coupling) software enables evaluation of electronic couplings based on the Förster model. PyFREC features the decomposition of electronic couplings, obtained through quantum chemical calculations, into the orientation and dipole strength components. Furthermore, the variation method to evaluate energies of coupled electronic excited states and delocalization of electronic excitations is implemented in the software. PyFREC has been tested on the S22 benchmark dataset of non‐covalent complexes and water clusters.