Robert W. Góra
Research interests
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InterestsQuantum Chemistry, Computational Chemistry, Quantum Mechanics, Intermolecular Interactions, Chemical Physics, Hydrogen Bonding
Publications
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2.90Impact points
On the Calculations of Interaction Energies and Induced Electric Properties within the Polarizable Continuum Model.
The journal of physical chemistry. A. 04/2012;
In this work we investigate the influence of polarizable environment on the interaction energies and the interaction--induced (excess) static electric dipole properties for the selected model hydrogen--bonded complexes. The excess properties were estimated for water and hydrogen fluoride dimers usin... [more] In this work we investigate the influence of polarizable environment on the interaction energies and the interaction--induced (excess) static electric dipole properties for the selected model hydrogen--bonded complexes. The excess properties were estimated for water and hydrogen fluoride dimers using the supermolecular approach and assuming the polarizable continuum model (PCM) as a representation of polarizable environment. We analyze in this context the performance of counterpoise correction and the consequences of various possible monomer cavity choices. The polarizable environment reduces the absolute magnitudes of interaction energies and interaction induced dipole moments, whereas an increase is observed for the absolute magnitudes of induced polarizabilities and first hyperpolarizabilities. Our results indicate that the use of either monomeric (MC) or dimeric (DC) cavities in calculations of monomer properties does not change qualitatively the resultant excess properties. We conclude that the DC scheme is more consistent with the definition of the interaction energy and consequently also the interaction--induced property, whereas the MC scheme corresponds to the definition of stabilization energy. Our results indicate also a good performance of the counterpoise correction scheme for the self--consistent methods in the case of all studied properties.
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2.90Impact points
Electronic structure, bonding, spectra, and linear and nonlinear electric properties of Ti@C28.
The journal of physical chemistry. A. 07/2011; 115(37):10370-81.
The potential energy surface (PES) of Ti@C(28) has been revisited, and the stationary points have been carefully characterized. In particular, the C(2v) symmetry structure considered previously turns out to be a transition state lying 2.3 kcal/mol above the ground state of C(3v) symmetry at the MP2/... [more] The potential energy surface (PES) of Ti@C(28) has been revisited, and the stationary points have been carefully characterized. In particular, the C(2v) symmetry structure considered previously turns out to be a transition state lying 2.3 kcal/mol above the ground state of C(3v) symmetry at the MP2/6-31G(d) level. A large binding energy of 181.3 kcal/mol is found at the ROMP2/6-31G(d) level. Topological analysis of the generalized Ti@C(28) density reveals four bond paths between Ti and carbon atoms of the host. The character of all four contacts corresponds to a partially covalent closed shell interaction. UV-vis, IR, and Raman spectra are calculated and compared with C(28)H(4). The dipole moment and the static electronic and double harmonic vibrational (hyper)polarizabilities have been obtained. Distortion of the fullerene cage due to encapsulation leads to nonzero diagonal components of the electronic first hyperpolarizability β, and to an increase in the diagonal components of the electronic polarizability α and second hyperpolarizability γ. However, introduction of the Ti atom causes a comparable or larger reduction in most cases due to localized bonding interactions. At the double harmonic level, the average vibrational β is much larger than its electronic counterpart, but the opposite is true for α and for the contribution to γ that has been calculated. There is also a very large anharmonic (nuclear relaxation) contribution to β which results from a shallow PES with four minima separated by very low barriers. Thus, the vibrational γ (and α) may, likewise, become much larger when anharmonicity is taken into account.
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2.90Impact points
Large changes of static electric properties induced by hydrogen bonding: an ab initio study of linear HCN oligomers.
The journal of physical chemistry. A. 05/2011; 115(18):4691-700.
We report the partitioning of the interaction-induced static electronic dipole (hyper)polarizabilities for linear hydrogen cyanide complexes into contributions arising from various interaction energy terms. We analyzed the nonadditivities of the studied properties and used these data to predict the ... [more] We report the partitioning of the interaction-induced static electronic dipole (hyper)polarizabilities for linear hydrogen cyanide complexes into contributions arising from various interaction energy terms. We analyzed the nonadditivities of the studied properties and used these data to predict the electric properties of an infinite chain. The interaction-induced static electric dipole properties and their nonadditivities were analyzed using an approach based on numerical differentiation of the interaction energy components estimated in an external electric field. These were obtained using the hybrid variational-perturbational interaction energy decomposition scheme, augmented with coupled-cluster calculations, with singles, doubles, and noniterative triples. Our results indicate that the interaction-induced dipole moments and polarizabilities are primarily electrostatic in nature; however, the composition of the interaction hyperpolarizabilities is much more complex. The overlap effects substantially quench the contributions due to electrostatic interactions, and therefore, the major components are due to the induction and exchange-induction terms, as well as the intramolecular electron-correlation corrections. A particularly intriguing observation is that the interaction first hyperpolarizability in the studied systems not only is much larger than the corresponding sum of monomer properties, but also has the opposite sign. We show that this effect can be viewed as a direct consequence of hydrogen-bonding interactions that lead to a decrease of the hyperpolarizability of the proton acceptor and an increase of the hyperpolarizability of the proton donor. In the case of the first hyperpolarizability, we also observed the largest nonadditivity of interaction properties (nearly 17%) which further enhances the effects of pairwise interactions.
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4.80Impact points
The Ethidium-UA/AU Intercalation Site: Effect of Model Fragmentation and Backbone Charge State
Journal of Chemical Theory and Computation. 01/2011; 7(8):2600-2609.
We report a systematic analysis of the intermolecular interactions of cationic ethidium intercalated into a UA/AU step of RNA for a single conformation based on crystallographic coordinates. Interaction energies at the MP2/6-31G** level were partitioned into electrostatic, exchange, delocalization, ... [more] We report a systematic analysis of the intermolecular interactions of cationic ethidium intercalated into a UA/AU step of RNA for a single conformation based on crystallographic coordinates. Interaction energies at the MP2/6-31G** level were partitioned into electrostatic, exchange, delocalization, and correlation components. Various pairwise interaction models built from chemically intuitive fragments reproduce within a few percent values obtained when treating the intercalation site as a whole. Gas phase results are very sensitive to the charge state of the two phosphate groups, with the electrostatic term nearly tripling when the counterions are removed. But this is largely compensated by solvation, an effect represented here within the polarizable continuum model. In a few cases, more diffuse and larger basis sets as well as QCISD(T) corrections were applied in an effort to estimate plausible ethidium-nucleobase electron correlation effects.
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3.47Impact points
Structural variability and the nature of intermolecular interactions in Watson-Crick B-DNA base pairs.
The journal of physical chemistry. B. 07/2010; 114(29):9629-44.
A set of nearly 100 crystallographic structures was analyzed using ab initio methods in order to verify the effect of the conformational variability of Watson-Crick guanine-cytosine and adenine-thymine base pairs on the intermolecular interaction energy and its components. Furthermore, for the repre... [more] A set of nearly 100 crystallographic structures was analyzed using ab initio methods in order to verify the effect of the conformational variability of Watson-Crick guanine-cytosine and adenine-thymine base pairs on the intermolecular interaction energy and its components. Furthermore, for the representative structures, a potential energy scan of the structural parameters describing mutual orientation of the base pairs was carried out. The results were obtained using the hybrid variational-perturbational interaction energy decomposition scheme. The electron correlation effects were estimated by means of the second-order Møller-Plesset perturbation theory and coupled clusters with singles and doubles method adopting AUG-cc-pVDZ basis set. Moreover, the characteristics of hydrogen bonds in complexes, mimicking those appearing in B-DNA, were evaluated using topological analysis of the electron density. Although the first-order electrostatic energy is usually the largest stabilizing component, it is canceled out by the associated exchange repulsion in majority of the studied crystallographic structures. Therefore, the analyzed complexes of the nucleic acid bases appeared to be stabilized mainly by the delocalization component of the intermolecular interaction energy which, in terms of symmetry adapted perturbation theory, encompasses the second- and higher-order induction and exchange-induction terms. Furthermore, it was found that the dispersion contribution, albeit much smaller in terms of magnitude, is also a vital stabilizing factor. It was also revealed that the intermolecular interaction energy and its components are strongly influenced by four (out of six) structural parameters describing mutual orientation of bases in Watson-Crick pairs, namely shear, stagger, stretch, and opening. Finally, as a part of a model study, much of the effort was devoted to an extensive testing of the UBDB databank. It was shown that the databank quite successfully reproduces the electrostatic energy determined with the aid of ab initio methods.
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3.47Impact points
On the Nature of Intermolecular Interactions in Nucleic Acid Base-Amino Acid Side-Chain Complexes.
The journal of physical chemistry. B. 08/2009;
Twenty hydrogen-bonded complexes composed of nucleic acid base and amino acid side chain have been analyzed using ab initio quantum chemistry methods with the aim of gaining insights into the nature of molecular interactions in these systems. The intermolecular interaction energies were estimated us... [more] Twenty hydrogen-bonded complexes composed of nucleic acid base and amino acid side chain have been analyzed using ab initio quantum chemistry methods with the aim of gaining insights into the nature of molecular interactions in these systems. The intermolecular interaction energies were estimated using the second-order Møller-Plesset perturbation theory and coupled clusters approach with single and double excitations, while their components have been determined by means of a hybrid variational-perturbational decomposition scheme. Additionally, the topological analysis of an electron density distribution of the studied complexes has been performed. In the case of all of the studied neutral complexes, the main source of stabilization is the delocalizaction energy associated with the electron density deformation upon the interaction which contributes almost half of the total interaction energy. Furthermore, analysis of the interaction induced difference density maps of complexes containing neutral amino acid side chains reveals that the delocalization component involves the electron density changes localized in the double-hydrogen-bonded ring structures. A relatively good correlation between the sum of densities at hydrogen-bond critical points and the Hartree-Fock intermolecular interaction energy components (electrostatic, delocalization, and exchange) has been observed for the two independently considered sets of complexes, containing positively charged and neutral amino acid side chains.
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2.29Impact points
On decomposition of interaction-induced electric properties of HF dimer
Chemical Physics Letters. 01/2008; 461(4-6):203-206.
Interaction energy in the linear HF dimer is calculated by means of the variational-perturbational scheme. Interaction-induced electric properties: dipole moment, polarizability and first-order hyperpolarizability are decomposed into the terms of physical meaning as the corresponding derivatives of ... [more] Interaction energy in the linear HF dimer is calculated by means of the variational-perturbational scheme. Interaction-induced electric properties: dipole moment, polarizability and first-order hyperpolarizability are decomposed into the terms of physical meaning as the corresponding derivatives of the interaction energy components. The distance dependence of the particular contributions to the interaction energy as well as to the electric properties is reported.
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2.29Impact points
The nature of interactions in uracil dimer: An ab initio study
Chemical Physics Letters. 01/2007; 450(1-3):132-137.
The intermolecular interaction energy components for the stacked uracil dimer have been evaluated at the MP2 level of theory using the variational-perturbational intermolecular interaction energy decomposition scheme. It was observed that the dispersion and electrostatic components are most dominant... [more] The intermolecular interaction energy components for the stacked uracil dimer have been evaluated at the MP2 level of theory using the variational-perturbational intermolecular interaction energy decomposition scheme. It was observed that the dispersion and electrostatic components are most dominant contributions to the stabilization energy. The former component does not exhibit the dependence on the mutual orientation of the uracil monomers, while for the latter strong directional variations have been found.
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2.29Impact points
On the cooperativity of the interaction-induced (hyper)polarizabilities of the selected hydrogen-bonded trimers
Chemical Physics Letters. 01/2007; 436(1-3):116-123.
The intermolecular interaction effects on the static electronic electric properties of three hydrogen-bonded systems (trimers of urea, fluoroacetylene and diformamide) have been investigated. The two- and three-body components of interaction-induced dipole moment, polarizability and first-order hype... [more] The intermolecular interaction effects on the static electronic electric properties of three hydrogen-bonded systems (trimers of urea, fluoroacetylene and diformamide) have been investigated. The two- and three-body components of interaction-induced dipole moment, polarizability and first-order hyperpolarizability have been calculated and analyzed at the SCF and MP2 levels of theory. The cooperativity of the three-body effects of the interaction-induced properties as well as the electron correlation effects have been investigated. In addition to the study of interaction-induced properties, the performance of recently developed polarized Z3Pol basis set has been tested against the following systematically extended Dunning's correlation consistent basis sets: aug-cc-pVDZ, aug-cc-pVTZ and d-aug-ce-pVDZ.
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3.09Impact points
On the influence of microsolvation by argon atoms on the electron affinity properties of water dimer.
The Journal of chemical physics. 04/2006; 124(9):94304.
This work provides a comparison of neutral (H2O)2Ar(n) and negatively charged (H2O)(2-)Ar(n) complexes. The excess electron stabilizes the complexes and leads to the trans to cis rearrangement within the water dimer core. In the case of small complexes (n < or = 4) the microsolvation of the dimer... [more] This work provides a comparison of neutral (H2O)2Ar(n) and negatively charged (H2O)(2-)Ar(n) complexes. The excess electron stabilizes the complexes and leads to the trans to cis rearrangement within the water dimer core. In the case of small complexes (n < or = 4) the microsolvation of the dimer by argon atoms arises on the trans side with respect to the donor water molecule. The stabilization of an excess electron is enhanced by the delocalization of the electronic charge density due to microsolvation. The process of cis to trans rotation is induced by the electric field of the approaching negative charge. The interaction energy decomposition suggests a more ionic character of binding in the negatively charged complexes. The attachment of an electron is controlled by the correlation energy.
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On the influence of intermolecular interactions on the electric properties of molecular aggregates
International Conference on Computational Methods in Science and Engineering; 01/2006
The systematic ab initio studies of intermolecular interaction energy components and linear and nonlinear optical properties of the selected model systems are considered. The influence of the external electric field due to the effective fragment potentials and(or) polarizable medium on the interacti... [more] The systematic ab initio studies of intermolecular interaction energy components and linear and nonlinear optical properties of the selected model systems are considered. The influence of the external electric field due to the effective fragment potentials and(or) polarizable medium on the interaction energy components and the electric properties of the studied systems is discussed. Furthermore the interaction induced molecular properties of the selected systems, obtained utilizing the finite field technique combined with the hybrid variational-perturbational interaction energy decomposition scheme, are reported and discussed focusing on their non-additivity and cooperativity.
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1.63Impact points
On the weak intermolecular interactions and their influence on the optical properties of unsaturated hydrocarbons. Part 1: Two- body interactions
Molecular Physics. 01/2006; 104(13-14):2263-2271.
The systematic ab initio studies of intermolecular interaction energy components in the model unsaturated hydrocarbon complexes have been performed. The influence of the weak intermolecular interactions on the optical properties has been analyzed within the supermolecular approach. The estimated int... [more] The systematic ab initio studies of intermolecular interaction energy components in the model unsaturated hydrocarbon complexes have been performed. The influence of the weak intermolecular interactions on the optical properties has been analyzed within the supermolecular approach. The estimated interaction energy components and electric properties of the studied systems indicate the substantial influence of the intermolecular forces on the optical response of the studied systems. The obtained results could be important for understanding the properties of the organic materials exploited for the purposes of the nonlinear optics.
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1.63Impact points
Proton bound open shell systems - theoretical studies on O2H+(O-2)(n) (n=1-6) complexes
Molecular Physics. 01/2006; 104(13-14):2327-2336.
Proton bound oxygen molecules form clusters, which are characterized by a symmetric O2H+O2 core and a second shell orthogonal to this core, with a possible capacity of up to five ligands. These clusters have been studied using density functional and Moller-Plesset (MP2) second-order perturbation the... [more] Proton bound oxygen molecules form clusters, which are characterized by a symmetric O2H+O2 core and a second shell orthogonal to this core, with a possible capacity of up to five ligands. These clusters have been studied using density functional and Moller-Plesset (MP2) second-order perturbation theories. The effect of dynamic correlation on the structures has been further studied on smaller clusters using a complete active space self-consistent field followed by multiconfigurational MP2 calculations. Calculations were performed for complexes resulting from coupling of interacting species to the highest possible spin momentum. The results show that the consecutive attachment of O-2 molecules stabilizes one of the two O-H+ bonds of the core with the simultaneous destabilization of the other. As the cluster grows the structure of the complexes changes from a symmetric OH+O core to a significantly asymmetric O2H+O-2(O-2)(5) cation with the OH+O bridge displaying the geometry of the conventional hydrogen bond. The nature of interactions and the bonding properties have been studied using a hybrid variational-peturbational scheme, natural bond orbital and atoms in molecule techniques. The hydrogen bonding in the complexes is of covalent nature and is only weakly influenced by the unpaired electrons of oxygen.
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2.90Impact points
Dimers of formic acid, acetic acid, formamide and pyrrole-2-carboxylic acid: an ab initio study.
The journal of physical chemistry. A. 08/2005; 109(29):6397-405.
The intermolecular hydrogen bonds in dimers of formic acid, acetic acid, and formamide were investigated. Additionally, three configurations of the pyrrole-2-carboxylic acid (PCA) dimer were studied to analyze how the pyrrole pi-electron system influences the carboxylic groups connected by double O-... [more] The intermolecular hydrogen bonds in dimers of formic acid, acetic acid, and formamide were investigated. Additionally, three configurations of the pyrrole-2-carboxylic acid (PCA) dimer were studied to analyze how the pyrrole pi-electron system influences the carboxylic groups connected by double O-H...O hydrogen bonds. The ab initio calculations for the systems investigated were performed at MP2/6-311++G(d,p), MP2/aug-cc-pVDZ, and MP2/aug-cc-pVTZ//MP2/aug-cc-pVDZ levels of theory. The "atoms in molecules" theory of Bader was used and the analysis of the critical points was performed to study the nature of hydrogen bonds. The decomposition of the total interaction energy applied here reveals that the delocalization energy term is a particularly important attractive contribution in these systems, more important in the case of systems forming homonuclear O-H...O double hydrogen bonds than in the case of those connected through heteronuclear N-H...O bonds. Because the systems analyzed may be formally classified as the resonance-assisted hydrogen bonds (RAHBs), it seems that the dominant contribution from the delocalization interaction energy term is a distinguished feature of such interactions.
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3.47Impact points
The nature of interactions in the ionic crystal of 3-pentenenitrile, 2-nitro-5-oxo, ion(-1), sodium.
The journal of physical chemistry. B. 03/2005; 109(5):2027-33.
The hybrid variation -- perturbation many-body interaction energy decomposition scheme has been applied to analyze the physical nature of interactions in the ionic 3-pentenenitrile, 2-nitro-5-oxo, ion(-1), sodium crystal, which can be regarded as a model for a large group of aromatic quaternary nitr... [more] The hybrid variation -- perturbation many-body interaction energy decomposition scheme has been applied to analyze the physical nature of interactions in the ionic 3-pentenenitrile, 2-nitro-5-oxo, ion(-1), sodium crystal, which can be regarded as a model for a large group of aromatic quaternary nitrogen salts. In the crystal structure the sodium ions and water molecules of adjacent unit cells form a positively charged "inorganic layer" with the sodium ions clustered together along the ab faces with the organic (negative) part in between. This puzzling crystal packing is due to a strong favorable interaction between the water molecule and the sodium ions and a substantial charge transfer from the carbanions that balances out the destabilizing sodium-sodium ion repulsion. Although the majority of cohesion energy of the crystal structure comes from the electrostatic interactions of ions, the resulting net stabilization also depends heavily on the nonadditive delocalization components, due to a counterbalance between the two-body delocalization and exchange effects. The estimated nonadditivity of interactions varies between 12% and 22%.
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2.29Impact points
On the influence of non-additive interactions on the optical properties of the selected subsystems of crystalline urea
Chemical Physics Letters. 01/2005; 406(1-3):29-37.
The results of many-body analysis of the intermolecular interaction energy for the selected subsystems of the molecular crystal of urea are discussed. In particular, a great importance of cooperative effects in both, the interaction energy and linear and non-linear optical properties are considered.... [more] The results of many-body analysis of the intermolecular interaction energy for the selected subsystems of the molecular crystal of urea are discussed. In particular, a great importance of cooperative effects in both, the interaction energy and linear and non-linear optical properties are considered. The nature of intermolecular interactions in the urea clusters is investigated applying the hybrid variational–perturbational interaction energy decomposition scheme. Molecular polarizabilities and first-order hyperpolarizabilities are estimated by means of a finite-field technique combined with the Hartree–Fock and the second-order Møller–Plesset perturbation theories. The results of our calculations indicate a substantial influence of the many-body effects on the non-linear response of the studied hydrogen-bonded systems.
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Theoretical Investigations of the Intermolecular Interactions between Unsaturated Hydrocarbons: π-cojugated and π-cumulated Oligomers
Annals Pol. Chem. Soc. 01/2005; 4:662-666.
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3.09Impact points
Intermolecular interactions in solution: elucidating the influence of the solvent.
The Journal of chemical physics. 03/2004; 120(6):2802-13.
A new approach for the analysis of intermolecular interactions in a solution is proposed. The changes in the interaction energy components due to the solvent effects are estimated on the basis of the interaction energy calculated in the presence of the electric field induced in a polarizable medium,... [more] A new approach for the analysis of intermolecular interactions in a solution is proposed. The changes in the interaction energy components due to the solvent effects are estimated on the basis of the interaction energy calculated in the presence of the electric field induced in a polarizable medium, or in the field of the effective fragment potentials. Obtained results indicate a significant increase in stabilization resulting from electrostatic interactions as a result of the cooperative interactions between interacting subsystems and solvent molecules.
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2.29Impact points
The micro-solvation of Na+: theoretical study of bonding characteristics in weakly bonded ArnNa+ (n=1-8) clusters
Chemical Physics Letters. 01/2004; 391(1-3):112-119.
New features of ArnNa+ clusters are revealed using reliable, accurate post-Hartree–Fock computations. Molecular geometries and harmonic vibrational frequencies of ArnNa+ (n=1–8) complexes are predicted at the MP2/6-311+G(3df) level of theory. Successive values of dissociation energy for all clusters... [more] New features of ArnNa+ clusters are revealed using reliable, accurate post-Hartree–Fock computations. Molecular geometries and harmonic vibrational frequencies of ArnNa+ (n=1–8) complexes are predicted at the MP2/6-311+G(3df) level of theory. Successive values of dissociation energy for all clusters were additionally calculated within the CCSD(T) approach. The nature of bonding in these structures is discussed based on natural population analysis and interaction energy decomposition scheme. A comprehensive discussion on the relevance of an appropriate treatment of core-valence electron correlation is provided for the ArNa+ ion. The presented data agrees well with the available experimental values.
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1.22Impact points
Theoretical ab initio study on the electronic states of GaO and Ga2O
Journal of Molecular Structure THEOCHEM. 01/2004; 672(1-3):105-111.
Potential energy curves have been calculated for the ground and excited doublet and quartet states of the radical gallium monoxide. The ground state, X2Σ+, is found to have a minimum at 1.65 Å with a well-depth of 4.65 eV, while the lowest excited state, A2Π is found to lie very close to the ground ... [more] Potential energy curves have been calculated for the ground and excited doublet and quartet states of the radical gallium monoxide. The ground state, X2Σ+, is found to have a minimum at 1.65 Å with a well-depth of 4.65 eV, while the lowest excited state, A2Π is found to lie very close to the ground state, at ν00 of 4204 cm−1 with rmin at 1.803 Å and a well depth of 4.06 eV. The next excited state, B2Σ+, which is the only excited state for which there is published experimental information, is well separated from the two lower states, with a shallow minimum of 1.81 eV calculated at 1.706 Å. Non adiabatic interactions between the three lowest electronic states of GaO are weak, and there is no significant mixing of the vibrational levels of the X2Σ+ and A2Π caused by rotational-electronic coupling, even for very high values of the rotational quantum number N. The present calculations support the earlier reported values for the rotational constants of the X2Σ+ and the B2Σ+ states rather than those of the more recent findings. Symmetric stretch potentials have been calculated for electronic states of the Gallium suboxide (Ga2O) molecule at linear geometries. The first excited state, A1Πu, is calculated at 5.03 eV above the ground electronic state, X1Σg+. The ground state and most of the excited states of Ga2O have minima at linear geometries.
Following (8)
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Paweł Lipkowski
University of Wroclaw -
Michał Marcin Jakób
Wroclaw University of Technology -
Antonio Rizzo
CNR - Consiglio Nazionale delle Ricerche -
Waclaw Andrzej Sokalski
Wrocław University of Technology -
Jaroslaw J Szymczak
Universität Basel
