Thermal and solvent effects on NMR indirect spin-spin coupling constants of a prototypical Chagas disease drug

NMR J-couplings across hydrogen bonds reflect the static and dynamic character of hydrogen bonding. They are affected by thermal and solvent effects and can therefore be used to probe such effects. We have applied density functional theory (DFT) to compute the NMR (n)J(N,H) scalar couplings of a prototypical Chagas disease drug (metronidazole). The calculations were done for the molecule in vacuo, in microsolvated cluster models with one or few water molecules, in snapshots obtained from molecular dynamics simulations with explicit water solvent, and in a polarizable dielectric continuum. Hyperconjugative and electrostatic effects on spin-spin coupling constants were assessed through DFT calculations using natural bond orbital (NBO) analysis and atoms in molecules (AIM) theory. In the calculations with explicit solvent molecules, special attention was given to the nature of the hydrogen bonds formed with the solvent molecules. The results highlight the importance of properly incorporating thermal and solvent effects into NMR calculations in the condensed phase.     

Simulations of the temperature dependence of amide I vibration

For spectroscopic studies of peptide and protein thermal denaturation it is important to single out the contribution of the solvent to the spectral changes from those originated in the molecular structure. To obtain insights into the origin and size of the temperature solvent effects on the amide I spectra, combined molecular dynamics and density functional simulations were performed with the model N-methylacetamide molecule (NMA). The computations well reproduced frequency and intensity changes previously observed in aqueous NMA solutions. An empirical correction of vacuum frequencies in single NMA molecule based on the electrostatic potential of the water molecules provided superior results to a direct density functional average obtained for a limited number of solute-solvent clusters. The results thus confirm that the all-atom quantum and molecular mechanics approach captures the overall influence of the temperature dependent solvent properties on the amide I spectra and can improve the accuracy and reliability of molecular structural studies.     

Solvent effects on peroxynitrite structure and properties from QM/MM simulations

We have investigated the structure and the vibrational spectrum of peroxynitrite anion in aqueous solution by means of combined quantum-classical (QM/MM) molecular dynamics simulations. In our QM/MM scheme, the reactant was modeled using density functional theory with a Gaussian basis set and the solvent was described using the mean-field TIP4P and the polarizable TIP4P-FQ force fields. The choice of basis sets, functionals and force field parameters has been validated by performing calculations on isolated peroxynitrite and on small peroxynitrite-water complexes. Poor values for isolated peroxynitrite structural properties and vibrational frequencies are found for most ab initio methods, particularly regarding the ON-OO(-) bond distance and the harmonic stretching frequency, probably due to the singlet-triplet instability found in the HF wave function. On the other hand, DFT methods yield results in better agreement with high level CCSD(T) ab initio calculations. We have computed the vibrational spectrum for aqueous peroxynitrite by calculating the Fourier transform of the velocity autocorrelation function extracted from the QM-MM molecular dynamics simulations. Our computational scheme, which allows for the inclusion of both anharmonicity and solvent effects, is able to clarify previous discrepancies regarding the experimental spectra assignments and to shed light on the subtle interplay between solvation and peroxynitrite structure and properties.     

Fluorescence spectra of organic dyes in solution: a time dependent multilevel approach

Classical all-atom molecular dynamics (MD) simulations and quantum mechanical (QM) time-dependent density functional theory (TD-DFT) calculations are employed to study the conformational and photophysical properties of the first emitter excited state of tetramethyl-rhodamine iso-thiocyanate fluorophore in aqueous solution. For this purpose, a specific and accurate force field has been parameterised from QM data to model the fluorophore's first bright excited state. During the MD simulations, the consequences of the π→π* electronic transition on the structure and microsolvation sphere of the dye has been analysed in some detail and compared to the ground state behaviour. Thereafter, fluorescence has been calculated at the TD-DFT level on configurations sampled from the simulated MD trajectories, allowing us to include time dependent solvent effects in the computed emission spectrum. The latter, when compared with the absorption spectrum, reproduces well the experimental Stokes shift, further validating the proposed multilevel computational procedure.     

Interpretation of synchrotron radiation circular dichroism spectra of anionic, cationic, and zwitterionic dialanine forms

Electronic absorption and synchrotron radiation circular dichroism (SRCD) spectra of the anionic, cationic, and zwitterionic forms of L-alanyl-L-alanine (AA) in aqueous solutions were measured and interpreted by molecular dynamics (MD) and ab initio computations. Time-dependent density functional theory (TD DFT) was applied to predict the electronic excited states. The modeling enabled the assessment of the role of molecular conformation, charge, and interaction with the polar environment in the formation of the spectral shapes. Particularly, inclusion of explicit solvent molecules in the computations appeared to be imperative because of the participation of water orbitals in the amide electronic structure. Implicit dielectric continuum solvent models gave inferior results for clusters, especially at low-energy transitions. Because of the dispersion of transition energies, tens of water/AA clusters had to be averaged in order to obtain reasonable spectral shapes with a more realistic inhomogeneous broadening. The modeling explained most of the observed differences, as the anionic and zwitterionic SRCD spectra were similar and significantly different from the cationic spectrum. The greatest deviation between the experimental and theoretical curves observed for the lowest-energy negative anion signal can be explained by the limited precision of the TD DFT method, but also by the complex dynamics of the amine group. The results also indicate that differences in the experimental spectral shapes do not directly correlate with the peptide main-chain conformation. Future peptide and protein conformational studies based on circular dichroic spectroscopy can be reliable only if such effects of molecular dynamics, solvent structure, and polar solvent-solute interactions are taken into account.     

NMR solvent shifts of acetonitrile from frozen density embedding calculations

We present a density functional theory (DFT) study of solvent effects on nuclear magnetic shielding parameters. As a test example we have focused on the sensitive nitrogen shift of acetonitrile immersed in a selected set of solvents, namely water, chloroform, and cyclohexane. To include the effect of the solvent environment in an accurate and efficient manner, we employed the frozen-density embedding (FDE) scheme. We have included up to 500 solvent molecules in the NMR computations and obtained the cluster geometries from a large set of conformations generated with molecular dynamics. For small solute-solvent clusters comparison of the FDE results with conventional supermolecular DFT calculations shows close agreement. For the large solute-solvent clusters the solvent shift values are compared with experimental data and with values obtained using continuum solvent models. For the water --> cyclohexane shift the obtained value is in very good agreement with experiments. For the water --> chloroform NMR solvent shift the classical force field used in the molecular dynamics simulations is found to introduce an error. This error can be largely avoided by using geometries taken from Car-Parrinello molecular dynamics simulations.     

The influence of solvation and finite temperatures on theWittig reaction: A theoretical study

The effects of the solvent and finite temperature (entropy) on the Wittig reaction are studied by using density functional theory in combination with molecular dynamics and a continuum solvation model. Standard gas-phase zero-temperature calculations are found to give similar results to previous studies. Gas-phase dynamics simulations allow the free energy profile of the reaction to be calculated through thermodynamic integration. The free energy profile is found to have a significant entropic barrier to the addition step of the reaction where only a small barrier was present in the potential energy curve. The introduction of the solvent dimethyl sulfoxide causes a change in the structure of the intermediate from the oxaphosphetane structure to the dipolar betaine structure. The overall reaction energy is changed only slightly. When the effects of both entropy and the solvent are included a significant entropic barrier to the addition reaction is obtained and the predicted intermediate again has the betaine structure.     

基于溶剂原位傅克偶联反应合成杯芳烃有机多孔网络(CalixPOF)及其染料吸附特性

利用1,2-二氯乙烷(DCE)同时作为溶剂和偶联剂,通过溶剂原位傅克偶联反应合成杯芳烃有机多孔网络(CalixPOF)。采用红外光谱(FT-IR)和固体核磁碳谱(13 C-NMR)对CalixPOF的组成和分子结构进行了表征,验证了溶剂原位Friedel-Crafts偶联反应机理。采用氮气吸附、扫描电镜(SEM)、热重(TG)和紫外可见光谱(UV-vis)研究了CalixPOF的比表面积、微观结构、热稳定性和染料吸附效率等性能。结果表明:利用简单的溶剂原位傅克偶联反应可得到热稳定性良好、比表面积较大、可选择性吸附亚甲基蓝染料的CalixPOF,为自具主客体微腔的新型多孔聚合物网络的合成提供了新方法。     

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     

Watching Na atoms solvate into (Na+,e-) contact pairs: untangling the ultrafast charge-transfer-to-solvent dynamics of Na- in tetrahydrofuran (THF)

With the large dye molecules employed in typical studies of solvation dynamics, it is often difficult to separate the intramolecular relaxation of the dye from the relaxation associated with dynamic solvation. One way to avoid this difficulty is to study solvation dynamics using an atom as the solvation probe; because atoms have only electronic degrees of freedom, all of the observed spectroscopic dynamics must result from motions of the solvent. In this paper, we use ultrafast transient absorption spectroscopy to investigate the solvation dynamics of newly created sodium atoms that are formed following the charge transfer to solvent (CTTS) ejection of an electron from sodium anions (sodide) in liquid tetrahydrofuran (THF). Because the absorption spectra of the sodide reactant, the sodium atom, and the solvated electron products overlap, we first examined the dynamics of the ejected CTTS electron in the infrared to build a detailed model of the CTTS process that allowed us to subtract the spectroscopic contributions of the sodide bleach and the solvated electron and cleanly reveal the spectroscopy of the solvated atom. We find that the neutral sodium species created following CTTS excitation of sodide initially absorbs near 590 nm, the position of the gas-phase sodium D-line, suggesting that it only weakly interacts with the surrounding solvent. We then see a fast solvation process that causes a red-shift of the sodium atom's spectrum in approximately 230 fs, a time scale that matches well with the results of MD simulations of solvation dynamics in liquid THF. After the fast solvation is complete, the neutral sodium atoms undergo a chemical reaction that takes place in approximately 740 fs, as indicated by the observation of an isosbestic point and the creation of a species with a new spectrum. The spectrum of the species created after the reaction then red-shifts on a approximately 10-ps time scale to become the equilibrium spectrum of the THF-solvated sodium atom, which is known from radiation chemistry experiments to absorb near approximately 900 nm. There has been considerable debate as to whether this 900-nm absorbing species is better thought of as a solvated atom or a sodium cation:solvated electron contact pair, (Na+,e-). The fact that we observe the initially created neutral Na atom undergoing a chemical reaction to ultimately become the 900-nm absorbing species suggests that it is better assigned as (Na+,e-). The approximately 10-ps solvation time we observe for this species is an order of magnitude slower than any other solvation process previously observed in liquid THF, suggesting that this species interacts differently with the solvent than the large molecules that are typically used as solvation probes. Together, all of the results allow us to build the most detailed picture to date of the CTTS process of Na- in THF as well as to directly observe the solvation dynamics associated with single sodium atoms in solution.     

Investigating the halochromic properties of azo dyes in an aqueous environment by using a combined experimental and theoretical approach

The halochromism in solution of a prototypical example of an azo dye, ethyl orange, was investigated by using a combined theoretical and experimental approach. Experimental UV/Vis and Raman spectroscopy pointed towards a structural change of the azo dye with changing pH value (in the range pH?5-3). The pH-sensitive behavior was modeled through a series of ab initio computations on the neutral and various singly and doubly protonated structures. For this purpose, contemporary DFT functionals (B3LYP, CAM-B3LYP, and M06) were used in combination with implicit modeling of the water solvent environment. Static calculations were successful in assigning the most-probable protonation site. However, to fully understand the origin of the main absorption peaks, a molecular dynamics simulation study in a water molecular environment was used in combination with time-dependent DFT (TD-DFT) calculations to deduce average UV/Vis spectra that take into account the flexibility of the dye and the explicit interactions with the surrounding water molecules. This procedure allowed us to achieve a remarkable agreement between the theoretical and experimental UV/Vis spectrum and enabled us to fully unravel the pH-sensitive behavior of ethyl orange in aqueous environment.     

Coherent two dimensional infrared spectroscopy of a cyclic decapeptide antamanide. A simulation study of the amide-I and A bands

The two-dimensional infrared photon echo spectrum of Antamanide (- (1)Val- (2)Pro- (3)Pro- (4)Ala- (5)Phe- (6)Phe- (7)Pro- (8)Pro- (9)Phe- (10)Pro-) in chloroform is calculated using an explicit solvent molecular dynamics (MD) simulation combined with a density functional theory (DFT) map for the effective vibrational Hamiltonian. Evidence for a strong intramolecular hydrogen bonding network is found. Comparison with experimental absorption allows the identification of the dominant conformation. Multidimensional spectroscopy reveals intramolecular couplings and gives information on its dynamics. A two-color amide-I and amide-A crosspeak is predicted and analyzed in terms of local structure.     

Solvent effects and dynamic averaging of 195Pt NMR shielding in cisplatin derivatives

The influences of solvent effects and dynamic averaging on the (195)Pt NMR shielding and chemical shifts of cisplatin and three cisplatin derivatives in aqueous solution were computed using explicit and implicit solvation models. Within the density functional theory framework, these simulations were carried out by combining ab initio molecular dynamics (aiMD) simulations for the phase space sampling with all-electron relativistic NMR shielding tensor calculations using the zeroth-order regular approximation. Structural analyses support the presence of a solvent-assisted "inverse" or "anionic" hydration previously observed in similar square-planar transition-metal complexes. Comparisons with computationally less demanding implicit solvent models show that error cancellation is ubiquitous when dealing with liquid-state NMR simulations. After aiMD averaging, the calculated chemical shifts for the four complexes are in good agreement with experiment, with relative deviations between theory and experiment of about 5% on average (1% of the Pt(II) chemical shift range).     

Nuclear magnetic shielding of the 113Cd(II) ion in aqua solution: a combined molecular dynamics/density functional theory study

We present a combined molecular dynamics simulation and density functional theory investigation of the nuclear magnetic shielding constant of the (113)Cd(II) ion solvated in aqueous solution. Molecular dynamics simulations are carried out for the cadmium-water system in order to produce instantaneous geometries for subsequent determination of the nuclear magnetic shielding constant at the density functional theory level. The nuclear magnetic shielding constant is computed using a perturbation theory formalism, which includes nonrelativistic and leading order relativistic contributions to the nuclear magnetic shielding tensor. Although the NMR shielding constant varies significantly with respect to simulation time, the value averaged over increasing number of snapshots remains almost constant. The paramagnetic nonrelativistic contribution is found to be most sensitive to dynamical changes in the system and is mainly responsible for the thermal and solvent effects in solution. The relativistic correction features very little sensitivity to the chemical environment, and can be disregarded in theoretical calculations when a Cd complex is used as reference compound in (113)Cd NMR experiments, due to the mutual cancelation between individual relativistic corrections.     

Solvent and concentration effects on the visible spectra of tri-para-dialkylamino-substituted triarylmethane dyes in liquid solutions

We have characterized the spectroscopy properties of crystal violet (CV+) and ethyl violet (EV+) in liquid solutions as a function of the solvent type and dye concentration. The analysis of how solvent properties and dye concentration affects the electronic spectra of these tri-para-dialkylamino substituted tryarylmethane (TAM+) dyes was performed on the basis of two spectroscopic parameters, namely the difference in wavenumber (deltanu) between the maximum and the shoulder that appears in the short-wavelength side of the respective maximum visible band (deltanu = 1/lambda(shoulder)-1/lambda(max) cm(-1)), and the wavelength of the maximum absorption (lambda(max)). The solvent and the concentration effects on lambda(max) and deltanu have indicated that both solute/solute (ion-pairing and dye aggregation) and solute/solvent (H-bonding type) interactions modulate the shape of the visible electronic spectra of these dyes in solution. In solvent with small dieletric constant (epsilon < approximately 10), the formation of ion-pairs represents a major contribution to the shaping of these spectra. Upon increasing dye concentration the formation of ion-pairs was characterized by an increase in deltanu observed concomitantly with a red shift in lambda(max) In chloroform and chlorobenzene the ion-pair association constant of CV+ and EV+ with Cl- ions were found to be in the order of 10(6) and 10(5) M(-1), respectively. In trichloroethylene the association constant for the CV+Cl- pair was 10(8) M(-1). In water, dye aggregation instead of ion-pairing represents a major contribution to the shaping of the visible spectra of CV+ and EV+. Dye aggregation was indicated by an increase in deltanu observed concomitantly with a blue shift in lambda(max) upon increasing dye concentration. The distinct behavior of deltanu for dye aggregation and ion-pairing as a function of dye concentration can therefore assist in the characterization of these two distinct phenomena. The solute/solvent interactions were studied in a series of polar solvents in which solute/solute interactions do not occur in any detectable extent. The dependence found for deltanu as a function of the Kamlet-Tafts solvatochromic parameters (alpha, beta and pi*) is in keeping with previous inferences indicating that the splitting in the overlapped absorption band of CV+ and EV+ in hydroxilated solvents arises from a perturbation in the molecular symmetry induced by hydrogen bonding (donor-acceptor) type interactions with solvent molecules. A distinction between the effects of solute/solute and solute/solvent interactions on the visible spectra of these dyes is provided.