scholarly journals Short-Range Imbalances in the AMBER Lennard-Jones Potential for (Deoxy)Ribose…Nucleobase Lone-pair…π Contacts in Nucleic Acids.

2021 ◽  
Author(s):  
Klaudia Mrazikova ◽  
Jiri Sponer ◽  
Vojtech Mlynsky ◽  
Pascal Auffinger ◽  
Holger Kruse
Keyword(s):  
Nucleic Acid ◽  
Short Range ◽  
Density Functional ◽  
Lone Pair ◽  
Md Simulations ◽  
Basis Set ◽  
Structural Motif ◽  
Lennard Jones ◽  
Π Stacking ◽  
Z Dna

The lone-pair…π (lp…π) (deoxy)ribose…nucleobase stacking is a recurring structural motif in Z DNA and RNAs that is characterized by sub-van der Waals lp…π contacts (<3.0 Å). It is part of the structural signature of the CpG Z-steps in Z-DNA and r(UNCG) tetraloops. These nucleic acid structures are poorly behaving in molecular dynamics (MD) simulations. Although the exact origin of these issues remains unclear, a significant part of the problem might be due to an imbalanced description of non-bonded interactions including the characteristic lp…π stacking. To gain insights into the links between lp…π stacking and MD issues, we present an in-depth comparison between accurate large-basis-set double-hybrid Kohn-Sham density functional theory calculations DSD-BLYP-D3/ma-def2-QZVPP (DHDF-D3) and data obtained with the non-bonded potential of the AMBER force field (AFF) for NpN Z-steps (N = G, A, C, U). Among other differences, we found that the AFF overestimates the DHDF D3 lp…π distances by ~0.1-0.2 Å while the deviation between the DHDF-D3 and AFF descriptions sharply increases in the short-range region of the interaction. Based on atom-in-molecule (AIM) polarizabilities and SAPT analysis, we inferred that the DHDF-D3 vs. AFF differences partly originate in the Lennard-Jones (LJ) parameters that are identical for nucleobase carbon atoms despite the presence/absence of connected electron withdrawing groups that lead to different effective volumes or vdW radii. Thus, to precisely model the very short CpG lp…π contact distances, we recommend revision of the nucleobase atom LJ parameters. Additionally, we suggest that the large discrepancy between DHDF-D3 and AFF short-range repulsive part of the interaction energy potential may significantly contribute to the poor performances of MD simulations of nucleic acid systems containing Z-steps. Understanding where, and if possible why, the point-charge-type effective potentials reach their limits is vital for developing next-generation FFs and for addressing specific issues in contemporary MD simulations.

Feasibility study of hydrogen-bonded nucleic acid base pairs in gas and water phases — A theoretical study

2011 ◽  
Vol 89 (11) ◽  
pp. 1403-1409 ◽  
Author(s):  
S. Arshadi ◽  
A.R. Bekhradnia ◽  
A. Ebrahimnejad
Keyword(s):  
Hydrogen Bonding ◽  
Nucleic Acid ◽  
Hydrogen Bonds ◽  
Density Functional ◽  
Biological Properties ◽  
Point Of View ◽  
Basis Set ◽  
Base Pairs ◽  
Bonding Properties ◽  
Energetic Point

To investigate the base pair binding probabilities for nucleic acid bases, numerous models were studied for contacts between adenine, thymine, guanine, cytosine, and uracil using density functional theory (DFT) in combination with the 6–311G* basis set. We obtained an assessment for the energy given by our calculations in gas and aqueous phases, which showed that it should be incorporated into hydrogen bonding and propeller rotational energies. The 42 complexes of base pairs (5 regular and 37 irregular base pairs) were proposed and their hydrogen-bonding (H-bonding) properties were verified. The hydrogen bonds in some irregular base pairs, including CC, UU, and TT (series 1), were stronger than in regular GC and AT base pairs. Also, the strength of the hydrogen bonds in the proposed base pairs, including CU, GG, GU, and TU (series 2), were similar to regular base pairs from an energetic point of view. The propeller rotations revealed a higher rotational barrier energy (6–7.5 kcal/mol; 1 cal = 4.184 J) for irregular base pairs (series 1 and 2) than regular GC and AT ones (1–3 kcal/mol). Nevertheless, the trend in these affinities of the complex contact probabilities and their biological properties were confirmed by our calculations.

scholarly journals Intermolecular Lennard-Jones (22-11)Potential Energy Surface in Dimer of N8 Cubane Cluster

2017 ◽  
Vol 59 (2) ◽  
Author(s):  
Jamshid Najafpour
Keyword(s):  
Potential Energy ◽  
Potential Energy Surface ◽  
Ab Initio ◽  
Density Functional ◽  
Energy Surface ◽  
Separation Distance ◽  
Basis Set ◽  
Intermolecular Potential ◽  
Basis Set Superposition Error ◽  
Lennard Jones

<p>We have calculated the intermolecular potential energy surface (IPES) of the dimer of cubic N8 cluster using <em>ab initio </em>and the density functional theory (DFT) calculations. The <em>ab initio </em>(HF/3- 21G(d)) and DFT (B3LYP/6-31G(d) and aug-cc-pVDZ) calculations were performed for two relative orientations of N8-N8 system as a function of separation distance between the centers of cubic N8 clusters. In this research, the IPES, <em>U</em>(<em>r</em>), of the N8-N8 system is studied, where the edge of N8 approaches to face or edge of the other considered N8. Then, the Lennard-Jones (12-6) and (22-11) adjustable parameters are fitted to the computed interaction energies for edge-face and edge-edge orientations. In this research for the first time, the IPESs proportionated to the Lennard-Jones (22-11) potential are derived that are compatible with the computed IPES curves. Assuming a set of Lennard-Jones parameters, the second virial coefficients are obtained for the N8-N8 complex at a temperature range of 298 to 1000 K. Both the corrected and uncorrected basis set superposition error (BSSE) results are presented confirming the significance of including BSSE corrections.</p>

scholarly journals In silico Evaluation of Cucurbit[6]uril as a Potential Detector for Cocaine and Its Adulterants Lidocaine, Caffeine, and Procaine

2021 ◽  
Author(s):  
Caio Rodrigues ◽  
Jorge Hernández-González ◽  
Natalia Pedrina ◽  
Vitor Leite ◽  
Aline Bruni
Keyword(s):  
In Silico ◽  
Density Functional ◽  
Illicit Drugs ◽  
Binding Free Energy ◽  
Md Simulations ◽  
Basis Set ◽  
Phase Condition ◽  
Cocaine Detection ◽  
Semi Empirical ◽  
And Control

Illicit drugs and their trafficking require worldwide efforts in investigation, detection, and control. Colorimetric tests are often applied to identify drugs. Cocaine has some well-known adulterants that can provide a false positive response. Cucurbit[6]uril (CB[6]) has been suggested as a potential detector for cocaine and other illicit drugs. This work uses in silico methods to evaluate the use of CB[6] to detect cocaine and these interfering substances. More specifically, this work analyzes different possibilities of CB[6] complexation with cocaine, lidocaine, caffeine, and procaine and compares the results achieved for cocaine and its adulterants. Different methodologies were employed: quantum chemistry was investigated through DFT B3LYP/TZVP (density functional theory-Becke, three-parameter, Lee-Yang-Parr with triple zeta valence plus polarization basis set) and the semi-empirical methods Austin model 1 (AM1), parametric methods 3, 6, and 7 (PM3, PM6, PM7), and Recife model 1 (RM1). We used these methodologies intending to compare the reasonability and reproducibility of the results in the gas phase condition. Solvent influence was studied by molecular dynamics (MD) simulations. Results showed that CB[6] does not bind to these substances, as judged from the positive values of binding free energy obtained with all methods. DFT and MD were the most reliable methods whereas semiempirical ones were not reproductible in describing these systems. Results also showed that interactions are not specific, so CB[6] does not provide a good response for cocaine detection.

Interatomic Potential and Thermodynamic Property of Diatomic Uranium

2012 ◽  
Vol 550-553 ◽  
pp. 2810-2813 ◽  
Author(s):  
Xiu Lin Zeng ◽  
Xue Hai Ju ◽  
Si Yu Xu
Keyword(s):  
Density Functional ◽  
Vibrational Energy ◽  
Interatomic Potential ◽  
Zero Point ◽  
Dft Method ◽  
Basis Set ◽  
Functional Theory ◽  
Lennard Jones ◽  
Anharmonicity Constant ◽  
The Relationship

Potential energy scan for U2 was performed by density functional theory (DFT) method at the B3LYP level in combination with the (ECP80MWB_AVQZ + 2f) basis set. The dissociation energy of U2, after being corrected for the zero-point vibrational energy, is 2.482 eV, which is in good agreement with the experiment. The calculated energy was fit to the typical potential functions of Morse, Lennard-Jones (L-J) and Rydberg. Both the Morse and Rydberg functions are good representatives of the potentials, but the Lennard-Jones function is not. The anharmonicity constant is very small. The anharmonic frequency is 113.99 cm–1. Thermodynamic properties of entropy and heat capacity at 298.2 K – 1500 K were calculated by using DFT-B3LYP computational results and Morse parameters, respectively. The relationship between entropy and temperature was established.

scholarly journals Density Functional Theory (DFT) and Natural Bond Orbital (NBO) Analysis of Intermolecular Hydrogen Bond Interaction in "Phosphorylated Nata De Coco - Water"

2018 ◽  
Vol 18 (1) ◽  
pp. 173 ◽  
Author(s):  
Sitti Rahmawati ◽  
Cynthia Linaya Radiman ◽  
Muhamad Abdulkadir Martoprawiro
Keyword(s):  
Density Functional Theory ◽  
Hydrogen Bond ◽  
Charge Transfer ◽  
Density Functional ◽  
Natural Bond Orbital ◽  
Intermolecular Hydrogen Bond ◽  
Lone Pair ◽  
Basis Set ◽  
Proton Acceptor ◽  
Functional Theory

This study aims to study the conformation, the hydrogen bond network, and the stabilities of all the possible intermolecular interactions in phosphorylated nata de coco membrane with water (NDCF-(H2O)n, n = 1-5). Analysis of natural bond orbital (NBO) was performed to measure the relative strength of the hydrogen bonding interactions, charge transfer, particularly the interactions of n-σ * O-H and to take into account the effect on the stabilities of the molecular structure. All calculation were performed using density functional theory (DFT) method, at B3LYP functional level of theory and 6-311 G** basis set. The charge transfer between the lone pair of a proton acceptor to the anti-bonding orbital of the proton donor provides the substantial to the stabilization of the hydrogen bonds. Interaction between NDCF and (H2O)5 was strongest with the stabilization energy of 37.73 kcal/mol, that indicate the ease of donating lone pair electrons. The contributions of each hydrogen bond to the stability of the complex have been analyzed.

Density functional theory, Comparative vibrational spectroscopic studies, HOMO-LUMO, and NBO analysis of Trichloro isocyanuric acid and Trithio cyanuric acid

2015 ◽  
Vol 8 (3) ◽  
pp. 2197-2221
Author(s):  
Theraviyum Chithambarathanu ◽  
M. Darathi ◽  
J. DaisyMagdaline ◽  
S. Gunasekaran
Keyword(s):  
Density Functional ◽  
Cyanuric Acid ◽  
Nbo Analysis ◽  
Basis Set ◽  
Potential Energy Distribution ◽  
Point Energy ◽  
Isocyanuric Acid ◽  
Ft Ir ◽  
Homo Lumo ◽  
Ft Raman

The molecular vibrations of Trichloro isocyanuric acid (C3Cl3N3O3) and Trithio cyanuric acid (C3H3N3S3) have been investigated in polycrystalline sample at room temperature by Fourier Transform Infrared (FT-IR) and FT-Raman spectroscopies in the region 4000-450 cm-1 and 4000-50 cm-1 respectively, which provide a wealth of structural information about the molecules. The spectra are interpreted with the aid of normal co-ordinate analysis following full structure optimization and force field calculations based on density functional theory   (DFT) using standard B3LYP / 6-311++ G (d, p) basis set for investigating the structural and spectroscopic properties. The vibrational frequencies are calculated and the scaled values are compared with experimental FT-IR and FT-Raman spectra. The scaled theoretical wave numbers shows very good agreement with experimental ones. The complete vibrational assignments are performed on the basis of potential energy distribution (PED) of vibrational modes, calculated with scaled quantum (SQM) method. Stability of the molecule arising from hyper conjugative interactions, charge delocalization has been analyzed using natural bond orbital (NBO) analysis. The results show that change in electron density (ED) in σ* and π* anti-bonding orbitals and second order delocalization   energy (E2) confirm the occurrence of Intra molecular Charge Transfer (ICT) within the molecule. The thermodynamic properties like heat capacity, entropy, enthalpy and zero point energy have been calculated for the molecule. The frontier molecular orbitals have been visualized and the HOMO-LUMO energy gap has been calculated. The Molecular Electrostatic Potential (MEP) analysis reveals the sites for electrophilic attack and nucleophilic reactions in the molecule.

Computationally Assisted Design of High Signal-to-Noise Photoinduced Electron Transfer-Based Voltage-Sensitive Dyes

2020 ◽  
Author(s):  
Rishikesh Kulkarni ◽  
Anneliese Gest ◽  
Chun Kei Lam ◽  
Benjamin Raliski ◽  
Feroz James ◽  
...  
Keyword(s):  
Electron Transfer ◽  
Dft Calculations ◽  
Photoinduced Electron Transfer ◽  
Density Functional ◽  
Embryonic Stem ◽  
High Sensitivity ◽  
Md Simulations ◽  
High Signal ◽  
Signal To Noise ◽  
Green Fluorescent

<p>High signal-to-noise optical voltage indicators will enable simultaneous interrogation of membrane potential in large ensembles of neurons. However, design principles for voltage sensors with high sensitivity and brightness remain elusive, limiting the applicability of voltage imaging. In this paper, we use molecular dynamics (MD) simulations and density functional theory (DFT) calculations to guide the design of a bright and sensitive green-fluorescent voltage-sensitive fluorophore, or VoltageFluor (VF dye), that uses photoinduced electron transfer (PeT) as a voltage-sensing mechanism. MD simulations predict an 11% increase in sensitivity due to membrane orientation, while DFT calculations predict an increase in fluorescence quantum yield, but a decrease in sensitivity due to a decrease in rate of PeT. We confirm these predictions by synthesizing a new VF dye and demonstrating that it displays the expected improvements by doubling the brightness and retaining similar sensitivity to prior VF dyes. Combining theoretical predictions and experimental validation has resulted in the synthesis of the highest signal-to-noise green VF dye to date. We use this new voltage indicator to monitor the electrophysiological maturation of human embryonic stem cell-derived medium spiny neurons. </p>

Evaluating Transition Metal Barrier Heights with the Latest DFT Exchange–Correlation Functionals – the MOBH35 Benchmark Dataset

2019 ◽  
Author(s):  
Mark Iron ◽  
Trevor Janes
Keyword(s):  
Transition Metal ◽  
Density Functional ◽  
Computational Cost ◽  
Basis Set ◽  
Functional Theory ◽  
Exchange Correlation ◽  
Barrier Heights ◽  
Complete Basis Set ◽  
Complete Basis Set Limit ◽  
Hybrid Functionals

A new database of transition metal reaction barrier heights – MOBH35 – is presented. Benchmark energies (forward and reverse barriers and reaction energy) are calculated using DLPNO-CCSD(T) extrapolated to the complete basis set limit using a Weizmann1-like scheme. Using these benchmark energies, the performance of a wide selection of density functional theory (DFT) exchange–correlation functionals, including the latest from the Truhlar and Head-Gordon groups, is evaluated. It was found, using the def2-TZVPP basis set, that the ωB97M-V (MAD 1.8 kcal/mol), ωB97X-V (MAD 2.1 kcal/mol) and SCAN0 (MAD 2.1 kcal/mol) hybrid functionals are recommended. The double-hybrid functionals PWPB95 (MAD 1.6 kcal/mol) and B2K-PLYP (MAD 1.8 kcal/mol) did perform slightly better but this has to be balanced by their increased computational cost.

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