A5074521314- Spectroscopy and Quantum Chemical Studies
- DNA and Nucleic Acid Chemistry
- Advanced Chemical Physics Studies
- Photochemistry and Electron Transfer Studies
- Crystallography and molecular interactions
- Various Chemistry Research Topics
- Click Chemistry and Applications
- Crystallization and Solubility Studies
- Advanced biosensing and bioanalysis techniques
- Photoreceptor and optogenetics research
- Photosynthetic Processes and Mechanisms
- X-ray Diffraction in Crystallography
- Experimental Learning in Engineering
- Chemical Synthesis and Analysis
- Protein Structure and Dynamics
- Mass Spectrometry Techniques and Applications
- Chemical Reaction Mechanisms
- Nanoplatforms for cancer theranostics
- Machine Learning in Materials Science
- Molecular spectroscopy and chirality
- bioluminescence and chemiluminescence research
- Photochromic and Fluorescence Chemistry
- Analytical Chemistry and Chromatography
- Origins and Evolution of Life
- Protein Interaction Studies and Fluorescence Analysis
Princeton University
2025
Monmouth University
2013-2023
Purdue University West Lafayette
2010-2021
Jackson State University
2007-2011
The Ohio State University
2010
Ames National Laboratory
2010
Iowa State University
2010
University of Southern California
2010
National Academy of Sciences of Ukraine
2007-2009
Institute of Molecular Biology and Genetics
2007-2009
A summary of the technical advances that are incorporated in fourth major release Q-Chem quantum chemistry program is provided, covering approximately last seven years. These include developments density functional theory methods and algorithms, nuclear magnetic resonance (NMR) property evaluation, coupled cluster perturbation theories, for electronically excited open-shell species, tools treating extended environments, algorithms walking on potential surfaces, analysis tools, energy...
This article summarizes technical advances contained in the fifth major release of Q-Chem quantum chemistry program package, covering developments since 2015. A comprehensive library exchange-correlation functionals, along with a suite correlated many-body methods, continues to be hallmark software. The methods include novel variants both coupled-cluster and configuration-interaction approaches based on algebraic diagrammatic construction variational reduced density-matrix methods. Methods...
Members of the green fluorescent protein (GFP) family form chromophores by modifications three internal amino acid residues. Previously, many key characteristics were studied using model compounds. However, no studies intermolecular excited-state proton transfer (ESPT) with GFP-like synthetic have been performed because they either are nonfluorescent or lack an ionizable OH group. In this paper we report synthesis and photochemical study two highly GFP chromophore analogues: p-HOBDI-BF2...
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 noncovalently bound systems. accuracy EFP benchmarked against S22 and S66 data sets noncovalent [Jurečka, P.; Šponer, J.; Černý, Hobza, P. Phys. Chem. Phys.2006, 8, 1985; Řezáč, Riley, K. E.; J. Theory Comput.2011, 7, 2427]. mean unsigned error (MUE) interaction energies with...
We report the use of bioorthogonal reactions as an original strategy in photodynamic therapy to achieve conditional phototoxicity and specific subcellular localization simultaneously. Our novel halogenated BODIPY-tetrazine probes only become efficient photosensitizers (ΦΔ ≈0.50) through intracellular inverse-electron-demand Diels-Alder reaction with a suitable dienophile. Ab initio computations reveal activation-dependent change decay channels that controls 1 O2 generation. approach also...
Solvatochromic shifts of the electronic states a chromophore can be used as measure solute-solvent interactions. The model organic chromophore, p-nitroaniline (pNA), embedded in solvents with different polarities (water, 1,4-dioxane, and cyclohexane) are studied using hybrid quantum mechanics/molecular-mechanics-type technique which is described by configuration interaction singles perturbative doubles (CIS(D)) method while solvent treated effective fragment potential (EFP) method. This...
The implementation of the effective fragment potential (EFP) method within Q-CHEM electronic structure package is presented. EFP used to study noncovalent π-π and hydrogen-bonding interactions in DNA strands. Since a computationally inexpensive alternative high-level ab initio calculations, it possible go beyond dimers nucleic acid bases investigate asymptotic behavior different components total interaction energy. calculations demonstrated that dispersion energy leading component π-stacked...
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 also describe the effect environment on electronic properties (e.g., excitation energies and ionization electron-attachment energies) subsystem via QM/EFP (quantum mechanics/EFP) embedding scheme. original formulation method assumes that system separated, without breaking covalent...
The single-conformation spectroscopy of two model γ-peptides has been studied under jet-cooled conditions in the gas phase. methyl-capped triamides, Ac-γ2-hPhe-γ2-hAla-NHMe and Ac-γ2-hAla-γ2-hPhe-NHMe, were probed by resonant two-photon ionization (R2PI) ion-dip infrared (RIDIR) spectroscopies. Four conformers three Ac-γ2-hAla-γ2-hPhe-NHMe observed spectroscopically interrogated. On basis comparison with predictions density functional theory calculations employing a dispersion-corrected...
A novel kinetic approach based on ab initio calculated rate constants has been developed and implemented in the kTSim program. The proposed allows prediction of distribution reactant product concentrations over time, exclusively computationally obtained constants. newly methodology was used to simulate process evaporation tautomerization guanine cytosine under thermal (T = 490 K, cytosine; T 620 guanine) laser 1000 24 ns pulse) desorption conditions. Both monomolecular bimolecular mechanisms...
Abstract A detailed description of the implementation effective fragment potential (EFP) method in Q‐CHEM electronic structure package is presented. The interfaces EFP with standard quantum mechanical (QM) methods such as Hartree–Fock, density functional theory, perturbation and coupled‐cluster methods, well for electronically excited open‐shell species, example, configuration interaction, time‐dependent equation‐of‐motion models. In addition to QM/EFP functionality, a “fragment‐only”...
We report how the conjugation of coelenterazine (CTZ) to BODIPY retains its activity as a versatile substrate for luciferase-type enzymes opening possibility taking advantage BODIPY's fluorescent properties and capacity generate singlet oxygen. Bioluminescence imaging-guided photodynamic therapy or 1O2-triggered drug release are potential applications these conjugates.
This project is designed to improve physical chemistry and instrumental analysis laboratory courses for undergraduate students by employing as teaching tools novel technologies in electronics data integration using the industrial Internet. The carried out upper-division undergraduates described. Students are exposed a complete process of building, calibrating, programming an automatic titrator open-source microcontroller platform standard pH probes, integrating instrument into approach...
Naphthalene diimide ligands have the potential to stabilize human telomeric G-quadruplex DNA via noncovalent interactions. Stabilization of high order structures has become an important strategy develop novel anticancer therapeutics. In this study four naphthalene based were analyzed in elucidate principal factors determining contributions G-quadruplex-ligand binding. Three possible modes binding and their respective Gibbs free energies for two di-N-alkylpyridinium substituted been...
A novel technology that employs computer vision (CV) to carry out an automatic titration experiment is presented. The designed facilitate understanding of the basics CV and its application in chemistry among undergraduate students. standard chemical procedure has been chosen, since it well-known students who completed general or similar foundation courses. significant advantage CV-based automation use open-source software readily available electronic devices, as no expensive specialized...
The tautomeric equilibrium and hydrogen bonding in nucleotide 2'-deoxyguanosine monophosphate that interacts with hydrated Mg2+ cation (4H2O.Mg[dGMP]) were studied at the MP2/cc-pVDZ//B3LYP/cc-pVDZ B3LYP/aug-cc-pVTZ//B3LYP/cc-pVDZ levels of theory. ion forms two inner-shell contacts nucleotide, similar to small phosphorylated molecules under physiological conditions. presence phosphate group magnesium leads a change guanine 4H2O.Mg[dGMP] comparison free guanine. influence on is larger anti...
The laboratory unit demonstrates a project-based approach to teaching physical chemistry where upper-division undergraduates carry out transient-absorption experiment investigating the kinetics of cis–trans isomerization N,N-dimethyl-4,4′-azodianiline. Students participate in modification standard flash-photolysis spectrometer by adding temperature-controlled sample holder. holder design is open-source and can be reproduced with 3D-printing technology. build experimental setup, perform...
The reported project-based laboratory unit introduces upper-division undergraduate students to the basics of computer-aided drug discovery as a part computational chemistry course. learn perform model binding organic molecules (ligands) DNA minor groove with (CADD) tools. purpose this is dock diminazene and its derivatives DNA, estimate their energies, elucidate details DNA–ligand intermolecular interactions. procedure also helps screen capabilities ligands.
Dynamics are intrinsic to both RNA function and structure. Yet, the available means precisely provide RNA-based processes with spatiotemporal resolution scarce. Here, our work pioneers a reversible approach regulate splicing within primary patient-derived cells by synthetic photoswitches. Our small molecule enables conditional real-time control at mRNA protein levels. NMR experiments, together theoretical calculations, photochemical characterization, fluorescence polarization measurements,...
Abstract Wir berichten über die Verwendung von bioorthogonalen Reaktionen als innovative Strategie in der photodynamischen Therapie, um gleichzeitig eine gezielte Phototoxizität und spezifische subzelluläre Lokalisation zu erreichen. Unsere neuartigen halogenierten BODIPY‐Tetrazin‐Sonden werden Gegenwart eines geeigneten Dienophils intrazelluläre Diels‐Alder‐Reaktion mit inversem Elektronenbedarf effizienten Photosensibilisatoren (Φ Δ ≈0.50). Ab‐initio‐Berechnungen zeigen...
High-level ab initio predictions of the tautomerization equilibrium and rate constants water-assisted proton transfer 1-methyl-cytosine (MeC) to its MeC* imino tautomeric form in presence up two water molecules (W) Na+ cation were carried out. The calculated energy values used obtain thermodynamic parameters concentration MeC, rare tautomer, their complexes with cation. for obtained by using instanton approach (a quasiclassical method based on least-action principle).(29) Hydration MeC one...
Excitation energy transfer (EET) determines the fate of sunlight absorbed by light‐harvesting proteins in natural photosynthetic systems and photovoltaic cells. As previously reported (D. Kosenkov, J. Comput. Chem . 2016, 37(19), 1847), PyFREC software enables computation electronic couplings between organic molecules with a molecular fragmentation approach. The present work reports implementation direct fragmentation‐based EET rates pigment–protein complexes within Förster theory new...
Electronic couplings are crucial for understanding exciton dynamics and associated energy transfer in artificial natural chromophores. The proposed PyFREC (Python FRagment Coupling) software enables evaluation of electronic based on the Förster model. features decomposition couplings, obtained through quantum chemical calculations, into orientation dipole strength components. Furthermore, variation method to evaluate energies coupled excited states delocalization excitations is implemented...
The DNA from Carcinoma Guerina resistant and sensitive cells of Wistar line rats their interaction with anti-cancer drugs—cis-platin doxorubicin (DOX)—have been studied in vivo experiments. Surface enhanced infrared absorption (SEIRA) reflectance–absorption spectroscopy (RAS) mode was applied for registration conformational change the induced by cancer process drugs. We have registered numerous minor changes spectra that could reflect essential molecular structure cells. most significant...
The naturally occurring modified nucleotide queuosine 5'-monophosphate (QMP) related to biochemical regulatory pathways in the cell was investigated using quantum chemical approaches. relative stability of biologically relevant conformations QMP solvent under a pH change predicted at BVP86/TZVP and MP2/TZVP levels theory. Hydrogen bonding studied Bader's approach. acidity constants were estimated COSMO-RS It has been found that neutral anionic forms are most stable physiological range. These...