Density functional theory study of 1:1 glycine-water complexes in the gas phase and in solution

The Resonance Raman Spectrum of Cytosine in Water: Analysis of the Effect of Specific Solute-Solvent Interactions and Non-Adiabatic Couplings

In this contribution, we report a computational study of the vibrational Resonance Raman (vRR) spectra of cytosine in water, on the grounds of potential energy surfaces (PES) computed by time-dependent density functional theory (TD-DFT) and CAM-B3LYP and PBE0 functionals. Cytosine is interesting because it is characterized by several close-lying and coupled electronic states, challenging the approach commonly used to compute the vRR for systems where the excitation frequency is in quasi-resonance with a single state. We adopt two recently developed time-dependent approaches, based either on quantum dynamical numerical propagations of vibronic wavepackets on coupled PES or on analytical correlation functions for cases in which inter-state couplings were neglected. In this way, we compute the vRR spectra, considering the quasi-resonance with the eight lowest-energy excited states, disentangling the role of their inter-state couplings from the mere interference of their different contributions to the transition polarizability. We show that these effects are only moderate in the excitation energy range explored by experiments, where the spectral patterns can be rationalized from the simple analysis of displacements of the equilibrium positions along the different states. Conversely, at higher energies, interference and inter-state couplings play a major role, and the adoption of a fully non-adiabatic approach is strongly recommended. We also investigate the effect of specific solute-solvent interactions on the vRR spectra, by considering a cluster of cytosine, hydrogen-bonded by six water molecules, and embedded in a polarizable continuum. We show that their inclusion remarkably improves the agreement with the experiments, mainly altering the composition of the normal modes, in terms of internal valence coordinates. We also document cases, mostly for low-frequency modes, in which a cluster model is not sufficient, and more elaborate mixed quantum classical approaches, in explicit solvent models, need to be applied.

Statistical Mechanics-Based Theoretical Investigation of Solvation Effects on Glucose Anomer Preferences

The importance of solvation effects on the stability of glucose anomers has been studied by the combination of quantum mechanics and statistical mechanics, namely, the reference interaction site model self-consistent field spatial electron density distribution. The preferences of α- and β-glucose in H₂O are well reproduced with the obtained ratio of 35:65 for α- and β-glucose, respectively. Indirect interactions and bulk effects, described by the Onsager model, are relatively small compared to the direct solute-solvent interactions, especially in [DMIM]Cl and dimethyl sulfoxide. From the decomposition of solvation free energy and solvation structures, it can be seen that the interactions with the solvent molecules greatly contribute to the anomer preferences.

Can THF hydrogen bond to glycine as strong as water?

Hydrogen bond complexation between glycine and THF and between glycine and water involving four lowest-energy glycine conformers have been studied. The complexes have been investigated in the gas phase at the ab initio molecular orbital theory (MP2) with aug-cc-pVDZ basis set and density functional theory (B3LYP) with aug-cc-pVTZ basis set. Bader’s theory of atoms in molecules (AIM), natural bond orbital (NBO), and symmetry adapted perturbation theory (SAPT) analyses are employed to elucidate the interaction characteristics in the complexes. The premise that the hydrogen bond donor ability of the O–H group of the carboxyl group dominates the interaction between glycine and THF and between glycine and water is confirmed. It is found that in comparison with water, THF binds more strongly to glycine. The quantum studies indicate that contribution of N–H···O and C–H···O hydrogen bonds in the complexes, although lower in magnitude to O–H···O interactions, play an important role in the stability of complexes. The blue and red shifts in the stretching frequencies of the hydrogen bond donors X–H (X = O, C, N) have also been related to stabilization energies. Decomposition of the stabilization energy based on the SAPT method clearly indicates the dominant role of the electrostatic interactions in all the complexes under study; however, induction and dispersion interaction terms are relatively higher in glycine–THF complexes.

Theoretical insight into the structural mechanism for the binding of vinblastine with tubulin

Vinblastine (VLB) is one of vinca alkaloids with high cytotoxicity toward cancer cells approved for clinical use. However, because of drug resistance, toxicity, and other side effects caused from the use of VLB, new vinca alkaloids with higher cytotoxicity toward cancer cells and other good qualities need to develop. One strategy is to further study and better understand the essence why VLB possesses the high cytotoxicity toward cancer cells. In present work, by using molecular simulation, molecular docking, density functional calculation, and the crystal structure of α,β-tubulin complex, we find two modes labeled in catharanthine moiety (CM) and vindoline moiety (VM) modes of VLB bound with the interface of α,β-tubulin to probe the essence why VLB has the high cytotoxicity toward cancer cells. In the CM mode, nine key residues B-Ser178, B-Asp179, B-Glu183, B-Tyr210, B-Asp226, C-Lys326, C-Asp327, C-Lys336, and C-Lys352 from the α,β-tubulin complex are determined as the active sites for the interaction of VLB with α,β-tubulin. Some of them such as B-Ser178, B-Glu183, B-Tyr210, B-Asp226, C-Lys326, C-Asp327, and C-Lys336 are newly identified as the active sites in present work. The affinity between VLB and the active pocket within the interface of α,β-tubulin is -60.8 kJ mol(-1) in the CM mode. In the VM mode, that is a new mode established in present paper, nine similar key residues B-Lys176, B-Ser178, B-Asp179, B-Glu183, B-Tyr210, B-Asp226, C-Lys326, C-Asp327, and C-Lys336 from the α,β-tubulin complex are found as the active sites for the interaction with VLB. The difference is from one key residue C-Lys352 in the CM mode changed to the key residue B-Lys176 in the VM mode. The affinity between VLB and the active pocket within the interface of α,β-tubulin is -96.3 kJ mol(-1) in the VM mode. Based on the results obtained in present work, and because VLB looks like two faces, composed of CM and VM both to have similar polar active groups, to interact with the active sites, we suggest double-faces sticking mechanism for the binding of VLB to the interface of α,β-tubulin. The double-faces sticking mechanism can be used to qualitatively explain high cytotoxicity toward cancer cells of vinca alkaloids including vinblastine, vincristine, vindestine, and vinorelbine approved for clinical use and vinflunine still in a phase III clinical trial. Furthermore, this mechanism will be applied to develop novel vinca alkaloids with much higher cytotoxicity toward cancer cells.

Short ligands offer long-term water stability and plasmon tunability for silver nanoparticles

Four short ligands; cysteine, cysteamine, dithiothrietol and glycine are examined and compared in their ability to stabilize and assemble silver nanoparticles (AgNPs).