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Imre G. Csizmadia - One of the best experts on this subject based on the ideXlab platform.

  • a prelude to building mathematical models for polypeptide folding analysis on the Conformational Potential energy hypersurface cross sections of n acetyl glycyl glycine n methylamide
    Canadian Journal of Chemistry, 2018
    Co-Authors: John Justine S Villar, Logine Negm, Anita Ragyanszki, David H Setiadi, Adrian Roy L Valdez, Bela Viskolcz, Imre G. Csizmadia
    Abstract:

    Finding a relationship on how a three-dimensional protein folds from its linear amino acid chain gets more complex with increasing chain length, so working on a smaller peptide Conformational problem can provide initial ideas on what are the main molecular forces and how these influence the folding process. Following the study of conformations of amino acid units entering the proteins to understand the secondary structure of small peptides, this paper proposes mathematical models for the several two-rotor cross-sections of the five-dimensional N-acetyl-glycyl-glycine-N′-methylamide Potential energy hypersurface (PEHS). These cross-sections are extracted along the first glycine subunit, with its coordinates fixed at the five energy minima of the glycine diamide. The resulting mathematical models yield an average RMSE of 1.36 kJ mol−1 and an average R2 of 0.9923 with respect to energy values obtained from DFT calculations. The minima geometries obtained from these models are also in good agreement with DFT-...

  • an improved two rotor function for Conformational Potential energy surfaces of 20 amino acid diamides
    Canadian Journal of Chemistry, 2018
    Co-Authors: John Justine S Villar, Anita Ragyanszki, David H Setiadi, Adrian Roy L Valdez, Bela Viskolcz, Imre G. Csizmadia
    Abstract:

    Predicting the three-dimensional structure of a protein from its amino acid sequence requires a complete understanding of the molecular forces that influences the protein folding process. Each possible conformation has its corresponding Potential energy, which characterizes its thermodynamic stability. This is needed to identify the primary intra- and intermolecular interactions, so that we can reduce the dimensionality of the problem, and create a relatively simple representation of the system. Investigating this problem using quantum chemical methods, albeit produces accurate results, this also entails large computational resources needed. In this study, an improved two-rotor Potential energy function is proposed to represent the backbone interactions in amino acids, through a linear combination of a Fourier series and a mixture of Gaussian functions. This function is applied to approximate the 20 amino acid diamide Ramachandran-type PESs, and results yielded an average RMSE of 2.36 kJ·mol -1 ,...

  • An improved two-rotor function for Conformational Potential energy surfaces of 20 amino acid diamides
    Canadian Journal of Chemistry, 2018
    Co-Authors: John Justine S Villar, David H Setiadi, Adrian Roy L Valdez, Bela Viskolcz, Imre G. Csizmadia, Anita Ragyanszki
    Abstract:

    Predicting the three-dimensional structure of a protein from its amino acid sequence requires a complete understanding of the molecular forces that influences the protein folding process. Each poss...

  • A prelude to building mathematical models for polypeptide folding: analysis on the Conformational Potential energy hypersurface cross-sections of N-acetyl-glycyl-glycine-N′-methylamide
    Canadian Journal of Chemistry, 2018
    Co-Authors: John Justine S Villar, Logine Negm, Anita Ragyanszki, David H Setiadi, Adrian Roy L Valdez, Bela Viskolcz, Imre G. Csizmadia
    Abstract:

    Finding a relationship on how a three-dimensional protein folds from its linear amino acid chain gets more complex with increasing chain length, so working on a smaller peptide Conformational probl...

  • dimension reduction in Conformational analysis a two rotor mathematical model of amino acid diamide Conformational Potential energy surface
    Canadian Journal of Chemistry, 2017
    Co-Authors: John Justine S Villar, Anita Ragyanszki, David H Setiadi, Adrian Roy L Valdez, Bela Viskolcz, Imre G. Csizmadia, Bela Fiser
    Abstract:

    The Conformational Potential energy surface (PES) of a molecule provides insights into the relative stability of the possible foldamers. However, the time and space complexity of electronic structure calculations, commonly used to generate PES, increases exponentially with an increasing number of atoms. The use of mathematical functions to model the topology of Conformational PES is an alternative to more computer-intensive quantum chemical calculations, but the choice and complexity of functions used are crucial in achieving more accurate results. This paper presents a method to illustrate the topology of amino acid diamide PESs through a linear combination of a Fourier series and a mixture of Gaussian functions. Results yield a significantly small error, with an average RMSE of 4.9946 kJ mol−1 for all fits, which suggest that these functions may be used to represent the topology of the PESs, with around twofold order of magnitude decrease in computational time, with respect to DFT electronic structure c...

András Perczel - One of the best experts on this subject based on the ideXlab platform.

  • An assessment of the chiral environment created by adjacent d- and l-alanyl residues on a glycine unit within the tripeptide N-Ac-Ala-Gly-Ala-NHMe: an ab initio exploratory study
    Journal of Molecular Structure: THEOCHEM, 2003
    Co-Authors: Jack C.c. Liao, Gregory A Chass, András Perczel, András Varró, John C Chua, Julius Gy. Papp
    Abstract:

    Ab initio Molecular Orbital computations were carried out on the tripeptide models, N-Ac-D-Ala-Gly-L-Ala-NHMe and NAc-L-Ala-Gly-L-Ala-NHMe at the RHF/3-21G level of theory. The topologies of Conformational Potential Energy Surfaces were explored and analyzed. In addition, global and local minima on the Ramachandran Potential Energy Surfaces, E ¼ f ðf1;c1) and E ¼ f ðf3;c3) were identified and their geometries optimized. The nearest neighboring effects of D and L amino acids on the conformations of the central glycine residue were also compared. Seven stable minima were found for each system and two conformers (a and 1) were oppositely different due to the influence of the N-terminal D -o rL-alanyl residue. q 2003 Elsevier Science B.V. All rights reserved.

  • N-acetyl-L-aspartic acid-N'-methylamide with side-chain orientation capable of external hydrogen bonding
    The European Physical Journal D - Atomic Molecular Optical and Plasma Physics, 2002
    Co-Authors: J.c.p. Koo, Gregory A Chass, Ladislaus L. Torday, Ödön Farkas, András Perczel, András Varró, J. Gy. Papp, I.g. Csizmadia
    Abstract:

    In this study, we generated and analyzed the side-chain Conformational Potential energy hypersurfaces for each of the nine possible backbone conformers for N-acetyl- L -aspartic acid-N' methylamide. We found a total of 27 out of the 81 possible conformers optimized at the B3LYP/6-31G(d) level of theory. The relative energies, as well as the stabilization energies exerted by the side-chain on the backbone, have been calculated for each of the 27 optimized conformers at this level of theory. Various backbone-backbone (N-H ^ . . . O=C) and backbone-side-chain (N-H ^ . . . O=C; N-H ^ . . . OH) hydrogen bonds were analyzed. The appearance of the notoriously absent backbone conformer may be attributed to such side-chain-backbone (SC/BB) and backbone-backbone (BB/BB) hydrogen bonds.

  • exploration of the four dimensional Conformational Potential energy hypersurface of n acetyl l aspartic acid n methylamide with its internally hydrogen bonded side chain orientation
    Journal of Physical Chemistry A, 2002
    Co-Authors: Gregory A Chass, Ladislaus L. Torday, Ödön Farkas, András Perczel, András Varró, Julius Gy. Papp, Imre G. Csizmadia
    Abstract:

    Side-chain Conformational Potential energy hypersurfaces have been generated and analyzed for each of the nine possible backbone conformers of N-acetyl-L-aspartic acid-N' methylamide. A total of 37 out of the 81 possible conformers were found and optimized at the B3LYP/6-31G(d) level of theory. The relative energies as well as the stabilization exerted by the side-chain on the backbone have been calculated, at this level of theory, for the 37 optimized conformers. Various backbone-backbone (N-H...O=C) and backbone-side-chain (N-H...O=C; N-H...OH) hydrogen bonds were analyzed. The appearance of the notoriously absent α L backbone conformer was attributed to such a backbone-side-chain (BB-SC) hydrogen bonds as well as a very unusual backbone-backbone (BB-BB) hydrogen bond.

  • Conformational effects of one glycine residue on the other glycine residues in the Ac-Gly-Gly-Gly-NHMe tripeptide motif: an ab initio exploratory study
    Journal of Molecular Structure-theochem, 2002
    Co-Authors: Azar Mehdizadeh, Gregory A Chass, Ladislaus L. Torday, Ödön Farkas, András Perczel, András Varró, Julius Gy. Papp
    Abstract:

    Abstract Ab initio molecular computations were carried out on the tripeptide model, Ac-Gly-Gly-Gly-NHMe at the RHF/3-21G ab initio level of theory. Two of the glycine residues were chosen at a time to be in the fully extended, or β (C 5 ) conformation, in order to monitor the effects on the third residue with varying the backbone conformation. The topologies of each of the three Ramachandran type Conformational Potential energy surfaces were analyzed and five minima (β, γ l , γ d , δ l , δ d ) associated with each one of the three glycine residues, were located for each surface.

  • N-acetyl-L-aspartic acid-N'-methylamide with side-chain orientation capable of external hydrogen bonding: Backbone and side-chain folding, studied at the DFT level of quantum theory
    The European Physical Journal D, 2002
    Co-Authors: J.c.p. Koo, Gregory A Chass, Ladislaus L. Torday, Ödön Farkas, András Perczel, András Varró, J. Gy. Papp, Imre G. Csizmadia
    Abstract:

    In this study, we generated and analyzed the side-chain Conformational Potential energy hypersurfaces for each of the nine possible backbone conformers for N-acetyl-L-aspartic acid-N' methylamide. We found a total of 27 out of the 81 possible conformers optimized at the B3LYP/6-31G(d) level of theory. The relative energies, as well as the stabilization energies exerted by the side-chain on the backbone, have been calculated for each of the 27 optimized conformers at this level of theory. Various backbone-backbone (N-H . . . O=C) and backbone-side-chain (N-H . . . O=C; N-H . . . OH) hydrogen bonds were analyzed. The appearance of the notoriously absent backbone conformer may be attributed to such side-chain-backbone (SC/BB) and backbone-backbone (BB/BB) hydrogen bonds.

David A. Brant - One of the best experts on this subject based on the ideXlab platform.

  • Influence of aqueous solvation on side chain-backbone interaction in comblike branched bacterial polysaccharides
    Macromolecules, 1994
    Co-Authors: Bjørn T. Stokke, Todd A. Talashek, David A. Brant
    Abstract:

    The solution behavior of regularly repeating branched bacterial copolysaccharides has been modeled using an approximate statistical mechanical treatment that accounts for the effects of side chain-backbone interactions on the Conformational freedom of the backbone glycosidic linkages. The probability distribution for glycosidic linkage orientations is based on pseudoindependent nearest-neighbor Conformational energy surfaces for each backbone linkage, perturbed by the influence of the side chain-backbone interaction. The influence of aqueous solvation has been investigated by using Conformational Potential energy functions that incorporate strong intrapolymeric hydrogen bonding to simulate weak solvation; stronger aqueous solvation is modeled by reducing the strength of the intramolecular hydrogen bonds

Ricardo D. Enriz - One of the best experts on this subject based on the ideXlab platform.

  • theoretical study of the Conformational energy hypersurface of cyclotrisarcosyl
    Central European Journal of Chemistry, 2012
    Co-Authors: Maria A. Álvarez, Fernando D. Suvire, Ricardo D. Enriz, Edgardo J Saavedra, Monica Olivella, Miguel A Zamora
    Abstract:

    The multidimensional Conformational Potential Energy Hypersurface (PEHS) of cyclotrisarcosyl was comprehensively investigated at the DFT (B3LYP/6-31G(d), B3LYP/6-31G(d,p) and B3LYP/6-311++G(d,p)), levels of theory. The equilibrium structures, their relative stability, and the Transition State (TS) structures involved in the Conformational interconversion pathways were analyzed. Aug-cc-pVTZ//B3LYP/6-311++G(d,p) and MP2/6-31G(d)//B3LYP/6-311++G(d,p) single point calculations predict a symmetric cis-cis-cis crown conformation as the energetically preferred form for this compound, which is in agreement with the experimental data. The Conformational interconversion between the global minimum and the twist form requires 20.88 kcal mol-1 at the MP2/6-31G(d)//B3LYP/6-311++G(d,p) level of theory. Our results allow us to form a concise idea about the internal intricacies of the PEHSs of this cyclic tripeptide, describing the conformations as well as the Conformational interconversion processes in this hypersurface. In addition, a comparative analysis between the Conformational behaviors of cyclotrisarcosyl with that previously reported for cyclotriglycine was carried out

  • ab initio and dft study of the Conformational energy hypersurface of cyclic gly gly gly
    Journal of Physical Chemistry A, 2009
    Co-Authors: Rodrigo D Tosso, Fernando D. Suvire, Miguel A Zamora, Ricardo D. Enriz
    Abstract:

    The multidimensional Conformational Potential energy hypersurface (PEHS) of cyclic Gly-Gly-Gly (1,4,7-triazonane-2,5,8-trione) was comprehensively investigated at the Hartree-Fock (RHF/6-31 G(d)) level of theory. The equilibrium structures, their relative stability, and the transition state (TS) structures involved in the Conformational interconversion pathways were analyzed. aug-cc-pVTZ/B3LYP/6-311++G** single point calculations predict a trans-cis-cis conformation as the energetically preferred form for this compound. However, all of the levels of theory employed here predicted that two forms, a trans-cis-cis and a cis-cis-cis (crown), of conformers contribute significantly to the equilibrium mixture at room temperature. The Conformational interconversion between the global minimum and the symmetric cis-cis-cis crown form requires 12.49 kcal/mol at the RHF 6-31G(d) level of theory, whereas the Conformational interconversion between the cis-cis-cis crown and cis-cis-cis boat form requires 18.70 kcal/mol. An exploratory topological analysis of the PEHS was also carried out. Our results allow us to form a concise idea about the internal intricacies of the PEHSs of these cyclic tripeptides, describing the conformations as well as the Conformational interconversion processes in these hypersurfaces.

  • A search for C–H⋯O type hydrogen bonds in Lamivudine (3TC). An exploratory Conformational and electronic analysis
    Journal of Molecular Structure-theochem, 2001
    Co-Authors: N.g. Fidanza, Fernando D. Suvire, Ricardo D. Enriz, Gladis L. Sosa, Rosana M. Lobayan, Nelida Maria Peruchena
    Abstract:

    Abstract A Conformational study of the molecule Lamivudine (3TC), or cis-1-[2′-hydroxymethyl-5′-(1,3-oxathiolanyl)] cytosine, was carried out. Rotation about the C–N bond (ϕ1) and about the C–CH2(OH) bond (ϕ2), which connects the hydroxymethyl group to the five member ring, led to a Conformational Potential energy surface. The Conformational Potential energy 2D map, obtained at the HF/3-21G level of theory, had several minima. A topological analysis of the electron density was carried out on four selected ab initio minimum energy conformations, using judiciously constructed hartree–fock (RHF) wave functions. In order to see all possible hydrogen bonding, the DFT wave function was generated using a mixed basis set; a 6-311++G∗∗ basis was employed on atoms involved in hydrogen bonding interactions and a 3-21G basis on all other atoms. For this analysis the theory of atoms in molecules, developed by Bader, was used. The stability of the intramolecular hydrogen bonding interactions was analyzed in terms of the results obtained.

  • An exploratory study of side-chain–backbone interaction in selected conformations of N-acetyl-l-glutamate-N-methylamide. An ab initio study
    Journal of Molecular Structure-theochem, 2001
    Co-Authors: Marcelo F. Masman, Fernando D. Suvire, Ödön Farkas, András Perczel, G.a. Chasse, M.g. Amaya, Ana M. Rodríguez, Ricardo D. Enriz
    Abstract:

    Abstract The Ramachandran map of N -acetyl- l -glutamate- N -methylamide has been explored using a, a side-chain (SC) conformation. Also, with fixed backbone (BB) conformations (γ l and β l ) the SC Conformational Potential energy surfaces were studied. The relative stabilities of the various conformers were analysed in terms of SC–BB interactions. The dynamic chirality of the glutamate SC was investigated and compared to that of the butyrate ion.

  • Dynamic chirality in selected diaryl methane containing drugs. An exploratory ab initio Conformational study
    Journal of Molecular Structure: THEOCHEM, 2001
    Co-Authors: Susana E Villagra, S. Zacchino, G.a. Chasse, Ana M. Rodríguez, M.b. Santillan, Mónica L. Freile, Péter Mátyus, Ricardo D. Enriz
    Abstract:

    Abstract Diaryl methane molecules (Ar–CH 2 –Ar) represent double rotor Conformational problems. The simplest diaryl methane, diphenyl methane (Ph–CH 2 –Ph), governs certain symmetric Conformational Potential energy surface (PES) topology. With the replacement of one of the phenyl groups by a heterocyclic moiety, the PES topology may change dramatically. The induction of point-chirality, in the prochiral CH 2 group, by axis-chirality or plane-chirality is explored within the framework of ‘dynamic chirality’.

Sandor Lovas - One of the best experts on this subject based on the ideXlab platform.

  • the role of weakly polar and h bonding interactions in the stabilization of the conformers of fgg wgg and ygg
    2009
    Co-Authors: Jozsef Csontos, Richard F. Murphy, Sandor Lovas
    Abstract:

    The energetics of intramolecular interactions on the Conformational Potential energy surface of the terminally protected N-Ac-Phe-Gly-Gly-NHMe (FGG), N-Ac-Trp-Gly-Gly-NHMe (WGG) and NAc-Tyr-Gly-Gly-NHMe (YGG) tripeptides was investigated. To identify the representative conformations, simulated annealing molecular dynamics (MD) and density functional theory (DFT) methods were used. The interaction energies were calculated at the BHandHLYP/aug-ccpVTZ level of theory. In the global minima, 10%, 31% and 10% of the stabilization energy come from weakly polar interactions, respectively, in FGG, WGG and YGG. In the prominent cases 46%, 62% and 46% of the stabilization energy is from weakly polar interactions, respectively, in FGG, WGG and YGG. On average, weakly polar interactions account for 15%, 34% and 9% of the stabilization energies of the FGG, WGG and YGG conformers, respectively. Thus, weakly polar interactions can make an important energetic contribution to protein structure and function.

  • the role of weakly polar and h bonding interactions in the stabilization of the conformers of fgg wgg and ygg an aqueous phase computational study
    Biopolymers, 2008
    Co-Authors: Jozsef Csontos, Richard F. Murphy, Sandor Lovas
    Abstract:

    The energetics of intramolecular interactions on the Conformational Potential energy surface of the terminally protected N-Ac-Phe-Gly-Gly-NHMe (FGG), N-Ac-Trp-Gly-Gly-NHMe (WGG), and N-Ac-Tyr-Gly-Gly-NHMe (YGG) tripeptides was investigated. To identify the representative conformations, simulated annealing molecular dynamics (MD) and density functional theory (DFT) methods were used. The interaction energies were calculated at the BHandHLYP/aug-cc-pVTZ level of theory. In the global minima, 10%, 31%, and 10% of the stabilization energy come from weakly polar interactions, respectively, in FGG, WGG, and YGG. In the prominent cases 46%, 62%, and 46% of the stabilization energy is from the weakly polar interactions, respectively, in FGG, WGG, and YGG. On average, weakly polar interactions account for 15%, 34%, and 9% of the stabilization energies of the FGG, WGG, and YGG conformers, respectively. Thus, weakly polar interactions can make an important energetic contribution to protein structure and function. © 2008 Wiley Periodicals, Inc. Biopolymers 89: 1002–1011, 2008. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com