The Joyce program is augmented with several new features, including the user friendly Ulysses GUI, possibility of complete excited state parameterization and a more flexible treatment force field electrostatic terms. A first validation achieved by successfully comparing results obtained Joyce2.0 to literature ones, for same set benchmark molecules. protocol also applied two other larger molecules, namely nicotine coumarin based dye. In former case, parameterized employed in molecular...

The spectroscopic properties of the organic chromophore 4-naphthoyloxy-1-methoxy-2,2,6,6-tetramethylpiperidine (NfO-TEMPO-Me) in toluene solution are explored through an integrated computational strategy combining a classical dynamic sampling with quantum mechanical description within framework time-dependent density functional theory (TDDFT) approach. atomistic simulations based on accurately parametrized force field, specifically designed to represent conformational behavior molecule its...

We explore the effect of solvent concentration on thermodynamic stability two polymorphs a 1:1 cocrystal theophylline and benzamide subjected to ball-mill liquid assisted grinding (LAG) we investigate how this can be related surface solvation phenomena. In system, most stable bulk polymorph form II converts metastable I upon neat (NG), while fully or partially transform into under LAG conditions, depending amount used. Careful strict experimental procedures were designed achieve equilibrium...

In this work, we present the derivation and implementation of analytical first second derivatives for a fully polarizable QM/MM/PCM energy functional. First with respect to both QM- MM-described nuclear coordinates electric perturbations are derived implemented, some preliminary application is shown. Analytical then derived, numerical test presented solvated system cromophore embedded in biological matrix.

Abstract Reactive oxygen species play an important role in cancer, however, their promiscuous reactivity, low abundance, and short-lived nature limit our ability to study them real time living subjects with conventional noninvasive imaging methods. Photoacoustic is emerging modality for vivo visualization of molecular processes deep tissue penetration high spatiotemporal resolution. Here, we describe the design synthesis a targeted, activatable probe photoacoustic imaging, which responsive...

The electronic absorption spectra of pyridine and nicotine in aqueous solution have been computed using a multistep approach. computational protocol consists studying the solute solvation with accurate molecular dynamics simulations, characterizing hydrogen bond interactions, calculating transitions for series configurations extracted from trajectories polarizable QM/MM scheme based on fluctuating charge model. Molecular simulations transition calculations performed both nicotine....

A robust and automated protocol for the derivation of sound force field parameters, suitable condensed-phase classical simulations, is here tested validated on several halogenated hydrocarbons, a class compounds which standard fields have often been reported to deliver rather inaccurate performances. The major strength proposed that all parameters are derived only from first principles because information required retrieved quantum mechanical data, purposely computed investigated molecule....

In classical molecular dynamics, general purpose atomistic force-fields (FFs) often deliver inaccurate results when dealing with halogen bonds (XBs), notwithstanding their crucial role in many fields of science, ranging from material design to drug development. Given the large dimensions systems interest, it would be therefore desirable increase FF accuracy maintaining simplicity standard Lennard-Jones (LJ) plus point charge description avoid an excessive computational cost. A simple yet...

The effect of complex embedding on the structural, dynamic and photophysical properties an organic dye were investigated using multi-layered computational methodology.

We present the SSIPTools suite of programs. is a collection software modules enabling use Surface Site Interaction Point (SSIP) molecular descriptors, used for modeling noncovalent interactions in neutral organic molecules. It contains an implementation workflow generation SSIP as well Functional Group Profiles (FGIPs) and Solvent Similarity Indexes (SSIs) applications, based on SSIMPLE (Surface model Properties Liquids at Equilibria) approach.

<div>Abstract<p>Reactive oxygen species play an important role in cancer, however, their promiscuous reactivity, low abundance, and short-lived nature limit our ability to study them real time living subjects with conventional noninvasive imaging methods. Photoacoustic is emerging modality for <i>in vivo</i> visualization of molecular processes deep tissue penetration high spatiotemporal resolution. Here, we describe the design synthesis a targeted, activatable probe...

<p>Supporting Methods Supporting Figures 1-11 Tables 1-3 Figure 1. Synthesis route for the smart, targeted hydrogen peroxide probe. Reagents and conditions: (a) 4-Bromo-1-butyne, NaI, MeCN, reflux. (b) POCl3, DMF. (c) Aniline, EtOH. (d) NaOAc, EtOH, (e) Piperazine, Cs2CO3, MeCN. (f) 1-Azido-1-deoxy-β-D-glucopyranoside, CuSO4, Na-ascorbate, t-BuOH, H2O. (g) 4-Nitrophenylchloroformate, Pyridine, DCM. (h) 4, DIPEA, (i) Cu(CH3CN)4, TBTA, ACN. 2. Calibration of LC-MS/MS study. This study...

<p>Supporting Methods Supporting Figures 1-11 Tables 1-3 Figure 1. Synthesis route for the smart, targeted hydrogen peroxide probe. Reagents and conditions: (a) 4-Bromo-1-butyne, NaI, MeCN, reflux. (b) POCl3, DMF. (c) Aniline, EtOH. (d) NaOAc, EtOH, (e) Piperazine, Cs2CO3, MeCN. (f) 1-Azido-1-deoxy-β-D-glucopyranoside, CuSO4, Na-ascorbate, t-BuOH, H2O. (g) 4-Nitrophenylchloroformate, Pyridine, DCM. (h) 4, DIPEA, (i) Cu(CH3CN)4, TBTA, ACN. 2. Calibration of LC-MS/MS study. This study...

<div>Abstract<p>Reactive oxygen species play an important role in cancer, however, their promiscuous reactivity, low abundance, and short-lived nature limit our ability to study them real time living subjects with conventional noninvasive imaging methods. Photoacoustic is emerging modality for <i>in vivo</i> visualization of molecular processes deep tissue penetration high spatiotemporal resolution. Here, we describe the design synthesis a targeted, activatable probe...