Towards Quantum-Chemical Modeling of the Activity of Anesthetic Compounds.

The modeling of the activity of anesthetics is a real challenge because of their unique electronic and structural characteristics. Microscopic approaches relevant to the typical features of these systems have been developed based on the advancements in the theory of intermolecular interactions. By stressing the quantum chemical point of view, here, we review the advances in the field highlighting differences and similarities among the chemicals within this group. The binding of the anesthetics to their partners has been analyzed by Symmetry-Adapted Perturbation Theory to provide insight into the nature of the interaction and the modeling of the adducts/complexes allows us to rationalize their anesthetic properties. A new approach in the frame of microtubule concept and the importance of lipid rafts and channels in membranes is also discussed.

Fentanyl Family at the Mu-Opioid Receptor: Uniform Assessment of Binding and Computational Analysis.

Interactions of 21 fentanyl derivatives with µ-opioid receptor (µOR) were studied using experimental and theoretical methods. Their binding to µOR was assessed with radioligand competitive binding assay. A uniform set of binding affinity data contains values for two novel and one previously uncharacterized derivative. The data confirms trends known so far and thanks to their uniformity, they facilitate further comparisons. In order to provide structural hypotheses explaining the experimental affinities, the complexes of the studied derivatives with µOR were modeled and subject to molecular dynamics simulations. Five common General Features (GFs) of fentanyls' binding modes stemmed from these simulations. They include: GF1) the ionic interaction between D147 and the ligands' piperidine NH⁺ moiety; GF2) the N-chain orientation towards the µOR interior; GF3) the other pole of ligands is directed towards the receptor outlet; GF4) the aromatic anilide ring penetrates the subpocket formed by TM3, TM4, ECL1 and ECL2; GF5) the 4-axial substituent (if present) is directed towards W318. Except for the ionic interaction with D147, the majority of fentanyl-µOR contacts is hydrophobic. Interestingly, it was possible to find nonlinear relationships between the binding affinity and the volume of the N-chain and/or anilide's aromatic ring. This kind of relationships is consistent with the apolar character of interactions involved in ligand⁻receptor binding. The affinity reaches the optimum for medium size while it decreases for both large and small substituents. Additionally, a linear correlation between the volumes and the average dihedral angles of W293 and W133 was revealed by the molecular dynamics study. This seems particularly important, as the W293 residue is involved in the activation processes. Further, the Y326 (OH) and D147 (Cγ) distance found in the simulations also depends on the ligands' size. In contrast, neither RMSF measures nor D114/Y336 hydrations show significant structure-based correlations. They also do not differentiate studied fentanyl derivatives. Eventually, none of 14 popular scoring functions yielded a significant correlation between the predicted and observed affinity data (R < 0.30, n = 28).

Structural Insights into σ1 Receptor Interactions with Opioid Ligands by Molecular Dynamics Simulations.

Despite considerable advances over the past years in understanding the mechanisms of action and the role of the σ1 receptor, several questions regarding this receptor remain unanswered. This receptor has been identified as a useful target for the treatment of a diverse range of diseases, from various central nervous system disorders to cancer. The recently solved issue of the crystal structure of the σ1 receptor has made elucidating the structure-activity relationship feasible. The interaction of seven representative opioid ligands with the crystal structure of the σ1 receptor (PDB ID: 5HK1) was simulated for the first time using molecular dynamics (MD). Analysis of the MD trajectories has provided the receptor-ligand interaction fingerprints, combining information on the crucial receptor residues and frequency of the residue-ligand contacts. The contact frequencies and the contact maps suggest that for all studied ligands, the hydrophilic (hydrogen bonding) interactions with Glu172 are an important factor for the ligands' affinities toward the σ1 receptor. However, the hydrophobic interactions with Tyr120, Val162, Leu105, and Ile124 also significantly contribute to the ligand-receptor interplay and, in particular, differentiate the action of the agonistic morphine from the antagonistic haloperidol.

Tailoring the Schiff base photoswitching - a non-adiabatic molecular dynamics study of substituent effect on excited state proton transfer.

Small molecular systems exhibiting Excited State Intramolecular Proton Transfer (ESIPT) attract considerable attention due to their possible role as ultrafast, efficient, and photostable molecular photoswitches. Here, by means of static potential energy profile scan and on-the-fly non-adiabatic dynamics simulations we study the photodeactivation process of a minimal-chromophore aromatic Schiff base, salicylidene methylamine (SMA), and its two derivatives 6-cyano-salicylidene methylamine (6-CN-SMA) and 3-hydroxy-salicylidene methylamine (3-OH-SMA). We show that the dominant character of the lowest excited singlet state - ππ* vs. nπ* - plays a crucial role in the system's photophysics and controls the ESIPT efficiency. We also show that the relative alignment of the ππ* and nπ* states may be controlled through chemical substitutions made to the aromatic ring of the Schiff-base molecule. We believe that our findings will improve the rational-design strategies employed for the ESIPT systems, especially in the context of their possible photoswitching.

Electric field control of proton-transfer molecular switching: molecular dynamics study on salicylidene aniline.

In this letter, we propose a novel, ultrafast, efficient molecular switch whose switching mechanism involves the electric field-driven intramolecular proton transfer. By means of ab initio quantum chemical calculations and on-the-fly dynamics simulations, we examine the switching performance of an isolated salicylidene aniline molecule and analyze the perspectives of its possible use as an electric field-controlled molecular electronics unit.

Excited-state intramolecular proton transfer: photoswitching in salicylidene methylamine derivatives.

The effect of chemical substitutions on the photophysical properties of the salicylidene methylamine molecule (SMA) (J. Jankowska, M. F. Rode, J. Sadlej, A. L. Sobolewski, ChemPhysChem, 2012, 13, 4287-4294) is studied with the aid of ab initio electronic structure methods. It is shown that combining π-electron-donating and π-electron-withdrawing substituents results in an electron-density push-and-pull effect on the energetic landscape of the ground and the lowest excited ππ* and nπ* singlet states of the system. The presented search for the most appropriate SMA derivatives with respect to their photoswitching functionality offers an efficient prescreening tool for finding chemical structures before real synthetic realization.

Photophysics of Schiff bases: theoretical study of salicylidene methylamine.

The proton-transfer reaction in a model aromatic Schiff base, salicylidene methylamine (SMA), in the ground and in the lowest electronically-excited singlet states, is theoretically analyzed with the aid of second-order approximate coupled-cluster model CC2, time-dependent density functional theory (TD-DFT) using the Becke, three-parameter Lee-Yang-Parr (B3LYP) functional, and complete active space perturbation theory CASPT2 electronic structure methods. Computed vertical-absorption spectra for the stable ground-state isomers of SMA fully confirm the photochromism of SMA. The potential-energy profiles of the ground and the lowest excited singlet state are calculated and four photophysically relevant isomeric forms of SMA; α, ß, γ, and δ are discussed. The calculations indicate two S(1)/S(0) conical intersections which provide non-adiabatic gates for a radiationless decay to the ground state. The photophysical scheme which emerges from the theoretical study is related to recent experimental results obtained for SMA and its derivatives in the low-temperature argon matrices (J. Grzegorzek, A. Filarowski, Z. Mielke, Phys. Chem. Chem. Phys. 2011, 13, 16596-16605). Our results suggest that aromatic Schiff bases are potential candidates for optically driven molecular switches.

Structure, energetics, and infrared spectra of weakly bound HC(2n+1)N···HCl complexes. A theoretical study.

Three model systems, HCN···HCl, HC(3)N···HCl, and HC(5)N···HCl, have been investigated computationally with the use of the second-order Möller-Plesset (MP2) and the coupled cluster (with single and double excitations and noniterative inclusion of triples) methods. The global minima are linear hydrogen-bonded structures with HCl as a proton donor. Bent structures are proton-side complexes with HCl as an electron donor, while the bifurcated hydrogen bonds are predicted for t-shape complexes. One of the most important findings in this paper is that, according to symmetry-adapted perturbation analysis, the induction-to-dispersion ratios are the biggest for linear complexes, and it is the most noticeable difference between linear, bent, and t-shape structures.

Thermal fluctuations and infrared spectra of the formamide-formamidine complex.

Combined effects of hydrogen bonding and thermal fluctuations on the structure and infrared spectra of the formamide-formamidine dimer, FM···FI, are studied using ab initio molecular dynamics simulations. The equilibrium structure of the dimer is stabilized by two hydrogen bonds that form a pattern reminiscent of that found in the adenine-thymine base pair. The structure of the hydrogen bonds at 300 K is subject to large fluctuations, with the hydrogen atom being tightly bound to the donor in the covalent bonding scenario. The hydrogen bond acceptor has a tendency to detach farther away from the D-H pair, approaching the dimer dissociation limit. Moreover, the N-H···O hydrogen bond breaks occasionally, thus giving rise to an "open" structure of the dimer, while the N-H···N bond stays largely intact at this temperature. Thermal fluctuations result in the minor red shifts of the monomer vibrational frequencies indicative of the anharmonicity of the potential energy surface. In contrast, the IR frequencies of the two symmetric NH(2) vibrational modes of the FM and FI monomers are shifted substantially toward the red upon hydrogen bond formation in the FM···FI dimer. Dynamical effects studied here are relevant, in particular, to the hydrogen bonding of nucleic acids at finite temperatures.

On vibrational circular dichroism chirality transfer in electron donor-acceptor complexes: a prediction for the quinine···BF3 system.

Vibrational circular dichroism (VCD) chirality transfer occurs when an achiral molecule interacts with a chiral one and becomes VCD-active. Unlike for H-bonds, for organic electron donor-acceptor (EDA) complexes this phenomenon remains almost unknown. Here, the VCD chirality transfer from chiral quinine to achiral BF3 is studied at the B3LYP/aug-cc-pVDZ level. Accessibility of four quinine electron donor sites changes with conformation. Therefore, the quinine conformational landscape was explored and a considerable agreement between X-ray and the most stable conformer geometries was achieved. The BF3 complex through the aliphatic quinuclidine N atom is definitely dominating and is predicted to be easily recognizable in the VCD spectrum. Out of several VCD chirality transfer modes, the ν(s)(BF3) mode, the most intense in the entire VCD spectrum, satisfies the VCD mode robustness criterion and can be used for monitoring the chirality transfer phenomenon in quinine···BF3 system.

Theoretical predictions of the spectroscopic parameters in noble-gas molecules: HXeOH and its complex with water.

We employ state-of-the-art methods and basis sets to study the effect of inserting the Xe atom into the water molecule and the water dimer on their NMR parameters. Our aim is to obtain predictions for the future experimental investigation of novel xenon complexes by NMR spectroscopy. Properties such as molecular structure and energetics have been studied by supermolecular approaches using HF, MP2, CCSD, CCSD(T) and MP4 methods. The bonding in HXeOH···H(2)O complexes has been analyzed by Symmetry-Adapted Perturbation Theory to provide the intricate insight into the nature of the interaction. We focus on vibrational spectra, NMR shielding and spin-spin coupling constants-experimental signals that reflect the electronic structures of the compounds. The parameters have been calculated at electron-correlated and Dirac-Hartree-Fock relativistic levels. This study has elucidated that the insertion of the Xe atom greatly modifies the NMR properties, including both the electron correlation and relativistic effects, the (129)Xe shielding constants decrease in HXeOH and HXeOH···H(2)O in comparison to Xe atom; the (17)O, as a neighbour of Xe, is deshielded too. The HXeOH···H(2)O complex in its most stable form is stabilized mainly by induction and dispersion energies.

Calculated nuclear magnetic resonance parameters for multiproton-exchange and nonbonded-hydrogen rotation processes in cyclic water clusters.

In this work we report, for the first time, calculations of nuclear magnetic resonance parameters for the processes of multiproton-exchange and nonbonded-proton rotations in small, cyclic water clusters. The simultaneous proton exchange induces a large decrease in the oxygen shielding constants in both clusters, with a mean value of -52.6 ppm for the water trimer and -50.1 ppm for the water tetramer. The (1(h))J(OH) coupling constant between an oxygen nucleus and exchanging proton decreases (in absolute value) along the path, changes sign, finally reaching a value of 5-7 Hz. The changes in the NMR parameters induced by the nonbonded proton rotations are smaller. The calculated dependencies of the intermolecular spin-spin coupling constants upon rotation reveal that the largest changes are expected for the couplings transmitted through the hydrogen bond between the rotating and neighboring molecule which acts as a proton donor. The symmetry-adapted perturbation theory (SAPT) interaction energy calculations for each dimer forming the water trimer have allowed us to relate a strength of interactions within pairs of water molecules with coupling constant values. The predicted maximal values of the interaction-energy terms (energetically unfavorable orientations of the constituent dimers) along paths correlate with the extremal values of the spin-spin coupling constants, which mostly correspond to the maximal couplings along pathways.

Nuclear magnetic resonance parameters for methane molecule trapped in clathrate hydrates.

The calculations of the nuclear shielding and spin-spin coupling constants were carried out for two models of clathrate hydrates, 5(12) and 5(12)6(8), using the density functional theory three-parameter Becke-Lee-Yang-Parr method with the basis set aug-cc-pVDZ (optimization) and HuzIII-su3 (NMR parameters). Particular attention has been devoted to evaluate the influence of a geometrical arrangement, the effect of long-range interactions on the NMR shielding of methane molecule, and to predict whether (13)C and (1)H chemical shifts can distinguish between guests in two clathrate hydrates cages. The correlation of the changes in the (17)O shielding constants depend strongly on the hydrogen-bonding topology. The intermolecular hydrogen-bond transmitted (1h)J(OH) spin-spin coupling constants are substantial. The increase of their values is connected with the elongation of the intramolecular O-H bond and the shortening of the intermolecular O···H distance. These data suggests that hydrogen bonds between double donor-single acceptor (DDA)-type water molecules acting as a proton acceptor from single donor-double acceptor (DAA)-type water molecules are stronger than ones formed by DAA-type water molecules acting as an acceptor for a DDA water proton. These state-of-the-art calculations confirmed the earlier experimental findings of the cage-dependency of (13)C chemical shift of methane.

VCD spectroscopy as a novel probe for chirality transfer in molecular interactions.

Most of the research in contemporary physical chemistry is devoted to the development of methods that extend our understanding, interpretation, and capacity to predict structural properties and dynamic behavior of molecules. The optical and magnetic spectroscopies, as well as diffraction techniques, are the principal methods for studying properties of molecules, biomolecules, and biopolymers of which the vast majority are chiral. On the other hand, information on molecular configuration can be obtained mainly from optical spectroscopies because other well-established spectroscopic techniques used for structural investigations, such as crystallographic, ESR, and NMR methods, do not allow for registration of signals from an individual conformer owing to intrinsic slow response to structural changes. This is the reason why the optical spectroscopy methods, based on natural chiroptical phenomena, have become so important and their renaissance in the last decade is noticed. Vibrational circular dichroism (VCD) spectroscopy is one such chiroptical technique that sheds new light on many important phenomena studied intensively. We provide an overview of recent theoretical predictions and innovative VCD observations of chirality transfer (called by other authors "induced chirality") from a chiral molecule to an achiral one as a result of hydrogen bond interactions between them. In this tutorial review we search for answers as to whether we can obtain further information about intermolecular interactions using the VCD technique. In our opinion this technique has opened new horizons for both understanding and monitoring intermolecular interactions and it could be used as a relatively new and powerful physicochemical method.

IR low-temperature matrix, X-ray and ab initio study on L-isoserine conformations.

The IR low-temperature Ar and Kr matrix spectra of l-isoserine were registered for the first time and interpreted by means of the anharmonic DFT frequencies calculated at the B3LYP/aug-cc-pVTZ and B3LYP/aug-cc-pVDZ levels. 54 l-isoserine conformers were predicted to be stable at the B3LYP/aug-cc-pVDZ level. Population of the 8 most stable conformers was based on the QCISD/aug-cc-pVDZ energies, corrected for thermal anharmonic factors obtained at the B3LYP/aug-cc-pVDZ level. We found several conformers to be present in the measured matrices and conformer 1 to be dominating. Presence of the conformer 2 is well confirmed by the nu(C=O) band at 1790 cm(-1) and two bands at 1380 and 1350 cm(-1). Presence of the conformer 4 is quite well confirmed by the nu(C-O) bands at 1120 and 1095 cm(-1). Slightly weaker arguments are found for the observation of conformers 6 and 3. Calculations on 54 neutral and 5 zwitterionic conformers in water at the IEF-PCM/B3LYP/aug-cc-pVDZ level suggest that one neutral and one zwitterionic conformer co-exist in the aqueous environment. The crystal structure of l-isoserine was solved by X-ray diffraction analysis. The compound crystallizes without solvent in the chiral P2(1)2(1)2 space group. The asymmetric unit contains a single molecule. The molecule is in its zwitterionic form with the CH(2)-NH(3) side chain in the gauche conformation with respect to the hydroxyl group and in the anti conformation with respect to the carboxylate group. The structure of l-isoserine is dominated by a set of intermolecular hydrogen bonds. The strongest one appears between the OH and COOH groups of two neighbouring molecules: the O...H contact is of 1.66(2) A, which is amongst the shortest H-bonds of this kind observed in amino acid crystal structures.

Theoretical study of the lactic acid-water system: importance of two- and three-body interactions.

Optimal structures, interaction energies, harmonic and anharmonic vibrational frequencies, and NMR chemical shifts of the dimers LA...H(2)O and trimers LA...(H(2)O)(2) (where LA is lactic acid) have been determined from the second-order Møller-Plesset perturbation theory and B3LYP with the aug-cc-pVDZ calculations. The nature of the pairwise and nonadditive three-body interactions was investigated by the SAPT method. As revealed by SAPT analysis, the main two-body binding contributions in the LA...H(2)O dimers and LA...(H(2)O)(2) trimers result from a delicate balance of the attractive and repulsive terms. The three-body nonadditivity for LA...(H(2)O)(2) is stabilizing and dominated by the exchange and induction effects but small.

A computational study of the nuclear magnetic resonance parameters for double proton exchange pathways in the formamide-formic acid and formamide-formamidine complexes.

In this paper, we present density functional theory calculations to predict the NMR parameters for two model systems: the formamide-formic acid (FM...FA) and formamide-formamidine (FM...FI) complexes, where intermolecular double proton exchange occurs. For the first time, the NMR parameters have been calculated along the reaction paths of the proton transfers described by means of the intrinsic reaction coordinate (IRC) procedure. The most interesting one-bond spin-spin coupling constants, (1(h))J(XH), between migrating protons and heavier nuclei change character from intra- to intermolecular along the pathway. The maximal positive values of the reduced (1(h))K(XH) coupling constants correspond to the situation when they are intramolecular; they decrease along the path, change sign and reach small negative values, becoming intermolecular couplings. The differing character of the double proton exchange resulting from the synchronicity or asynchronicity of the process is reflected in the calculated NMR parameters. Surprisingly substantial values have been calculated for the six-bond intermolecular proton-proton (6h)J(HH) coupling constants between protons bound to the carbon atoms. A simple procedure consisting of removal of the proton(s) forming the hydrogen bonds has been employed to indicate an influence of hydrogen bonding on the intermolecular coupling constants. Some of the spin-spin coupling constants ((2h)J(XY)) are predominantly transmitted through hydrogen bonds and decrease with removal of the proton(s), while others ((4h)J(CC)) are less sensitive to the presence or absence of the protons of hydrogen bonding.

The water-nitric oxide intermolecular potential-energy surface revisited.

The two lowest energy intermolecular potential-energy surfaces (IPESs) of the water-nitric oxide complex are evaluated using the spin-restricted coupled-cluster R-CCSD(T) model and the augmented correlation-consistent polarized-valence triple-zeta basis set extended with a set of the 3s3p2d1f1g midbond functions. A detailed characterization of the IPESs for both the (2)A(') and (2)A(") electronic states in the C(s)-symmetry configurations of the complex is performed. The global minimum for the (2)A(') state represented by the lowest energy of -461.8 cm(-1) is deeper than the global minimum in the (2)A(") state with an energy of -435.2 cm(-1). To explore the physics of the interaction an open-shell implementation of the symmetry-adapted perturbation theory is employed and the results are analyzed as a function of the intermolecular parameters. The electrostatic term shows the strongest geometric anisotropy, while the exchange, induction, and dispersion contributions mostly depend on the intermolecular distance. The energy separation between the (2)A(') and (2)A(") states is largely dominated by electrostatic contribution for long intermolecular distances. In the region of short intermolecular distances the exchange part is as important as the electrostatic one and the induction and dispersion effects are also substantial.

Molecular dynamics of fentanyl bound to µ-opioid receptor.

The molecular dynamics simulations of fentanyl complexed with the µ-opioid receptor (µOR) were studied using both inactive 4DKL and active 5C1M opioid receptor crystal structures. Analogous simulations in morphine with or without a ligand were done for comparison. Simulations of the inactive states were carried out in the absence and presence of the Na+ ion. The obtained fentanyl's binding mode agrees with some of the mutagenesis data, and it overlaps with that of morphine only to a minor extent. Notably, fentanyl stabilizes different rotameric states of Trp2936.48 than observed for morphine or unliganded receptor. Another difference is tighter arrangement of the interaction between Asp1473.32 and Tyr3267.43 (a link between helices TM3 and TM7) in the presence of fentanyl. Principal component analysis reveals differences in the trajectories dependent on the ligand bound. The differences found could be linked to ligand-dependent efficacy with respect to receptor intracellular signaling events.

Affinity of fentanyl and its derivatives for the σ1-receptor.

Fentanyl and its 11 commercially available derivatives were investigated as to their affinity for the σ1 receptor. The parent compound is a rather poor binder (IC50 = 4973 nM), but its close derivatives (benzylfentanyl or p-fluorofentanyl) have submicromolar affinities. Modelling provides a structural basis for the observed trends in activity.