Potential Energy Hypersurface Research Articles

The relative stability of the two isomers of AlP 3

The relative stability of the two lowest singlet states of AlP 3 (C 2V and C S symmetries) is studied using high-level ab initio calculations. Extrapolation to the infinite basis set limit using CCSD(T)/cc-pVXZ (X = 2, 3, 4 and 5) give the energy difference as 1.6 kcal/mol, with the C 2V structure lying lowest. Triple excitation contribution to the electron correlation effect and large basis sets are found to be very important. The locations of the two states on the potential energy hyper-surface are obtained to show that they represent well-defined and stable isomers.

Magnetism and the potential energy hypersurfaces of Fe53 to Fe57

We investigate magnetic and structural properties of iron clusters from Fe53 to Fe57 around the first peak in the experimental magnetic moment data at Fe55. A density-functional based tight-binding scheme, fully incorporating the effects of spin-polarization and charge transfer in a self-consistent manner, has been used. The potential hypersurfaces have been scanned by an unconstrained search using a genetic algorithm. We find icosahedral structures to be energetically favorable. These clusters show non-ferromagnetic spin-ordering leading to small average magnetic moments in their ground states. We establish a connection between the magnetic moments and the perturbation of icosahedral symmetry. This is interpreted further on the level of atomic spin-populations by examining the magnetic behavior of the Fe55 icosahedron.

Topography of the Potential Energy Hypersurface and Criteria for Fast-Ion Conduction in Perovskite-Related A2B2O5 Oxides

We discuss the importance of the topography of the potential energy hypersurface for the ionic conductivity of perovskite-related A(2)B(2)O(5) oxides. A correlation between the energetic preference of the cations for different coordination geometries and the ionic conductivity is proposed based on a first principles periodic density functional theory study of selected possible structures for Ba(2)In(2)O(5), Sr(2)Fe(2)O(5), Sr(2)Mn(2)O(5), and La(2)Ni(2)O(5). There are a large number of low-energy local minima on the potential energy hypersurfaces of the two first compounds due to an energetic preference for BO(4) tetrahedra. Tetrahedral environments are energetically unfavorable for Mn(III) in Sr(2)Mn(2)O(5) and for Ni(II) in La(2)Ni(2)O(5), and the number of low-energy configurations is relatively low in these two cases. Consistent with our findings, in contrast to Sr(2)Fe(2)O(5) and Ba(2)In(2)O(5), Sr(2)Mn(2)O(5) and La(2)Ni(2)O(5) do not exhibit transitions to disordered phases on heating, and there appear to be no reports of enhanced ionic conductivity for these compounds. Thus we suggest that the possibility of many different oxygen orderings associated with a variety of low-energy connectivity schemes within tetrahedral layers such as in the brownmillerite-based structures of Sr(2)Fe(2)O(5) and Ba(2)In(2)O(5) is a prerequisite for high ionic conductivity in perovskite-related A(2)B(2)O(5) oxides.

Comprehensive conformational analysis of N-acetyl- l-tryptophane- N-methylamide. An ab initio and DFT study

A comprehensive conformational analysis has been carried out on N-acetyl- l-tryptophane- N-methylamide. The complete set of minima has been located on the Potential Energy Hypersurface (PEHS) using ab initio (RHF/6-31G(d)) and DFT (B3LYP/6-31G(d)) calculations. Previous ab initio structure determinations at the RHF/3-21G level of theory resulted in 36 different structures. In the present work, a total of 35 and 34 different conformations were obtained at RHF/6-31G(d) and DFT (B3LYP/6-31G(d)) levels, respectively. Diamide conformers, similar to structural building units of the right-handed helix (α L) as well as of polyproline II type structures (ε L) were found. However, C 7 eq (γ L) and extended C 5 (β L) conformations were the preferred forms for this compound. Sidechain structural (i.e. χ 1 and χ 2 conformer interconversions) are also discussed in this paper.

Density functional theory study of the hydrogen bonding interaction in formamide dimer

The hydrogen bonding of 1:1 complexes formed between formamide and formamide molecule has been completely investigated in the present study using density functional theory (DFT) method at varied basis set levels from 6-31G to 6-311++G(2d,2p). The large basis sets 6-311++G(d,p) and 6-311++G(2d,2p) have been employed to determine the equilibrium structure and vibrational frequencies of the interacting complexes. Five reasonable geometries on the potential energy hypersurface of formamide dimer system are considered with the global minimum, four of which are cyclic double-hydrogen bonded structure and one is one-hydrogen bonded structure. The optimized geometric parameters and interaction energies for various isomers at different levels are estimated. The infrared spectrum frequencies, IR intensities and the vibrational frequency shifts are reported. Finally the solvent effects on the geometries of the formamide dimer have also been investigated using self-consistent reaction-field (SCRF) calculations at the B3LYP/6-311++G** level. The results indicate that the polarity of the solvent has played an important role on the structures and relative stabilities of different isomers.

The importance of tunneling in the first hydrogenation step in ammonia synthesis over a Ru(0001) surface

The hydrogenation of nitrogen (N(ads)+H(ads)-->NH(ads)) on metal surfaces is an important step in ammonia catalysis. We investigate the reaction dynamics of this hydrogenation step by time independent scattering theory and variational transition state theory (VTST) including tunneling corrections. The potential energy surface is derived by hybrid density functional theory on a model cluster composed of 12 ruthenium atoms resembling a Ru(0001) surface. The scattering calculations are performed on a reduced dimensionality potential energy hypersurface, where two dimensions are treated explicitly and all others are included implicitly by the zero-point correction. The VTST calculations include quantum effects along the reaction coordinate by applying the small curvature tunneling scheme. Even at room temperature (where ruthenium already shows catalytic activity) we find rate enhancement by tunneling by a factor of approximately 70. Inspection of the reaction probabilities shows that the major contribution to reactivity comes from the vibrational ground state of the reactants into vibrationally excited product states. The reaction rates are higher than determined in previous studies, and are compatible with experimental overall rates for ammonia synthesis.

A new pathway for the rapid decay of electronically excited adenine

Combined density functional and multireference configuration interaction methods have been used to calculate the electronic spectrum of 9H-adenine, the most stable tautomer of 6-aminopurine. In addition, constrained minimum energy paths on excited potential energy hypersurfaces have been determined along several relaxation coordinates. The minimum of the first (1)[n-->pi*] state has been located at an energy of 4.54 eV for a nuclear arrangement in which the amino group is pyramidal whereas the ring system remains planar. Close by, another minimum on the S(1) potential energy hypersurface has been detected in which the C(2) center is deflected out of the molecular plane and the electronic character of S(1) corresponds to a nearly equal mixture of (1)[pi-->pi*] and (1)[n-->pi*] configurations. The adiabatic excitation energy of this minimum amounts to 4.47 eV. Vertical and adiabatic excitation energies of the lowest n-->pi* and pi-->pi* transitions as well as transition moments and their directions are in very good agreement with experimental data and lend confidence to the present quantum chemical treatment. On the S(1) potential energy hypersurface, an energetically favorable path from the singlet n-->pi* minimum toward a conical intersection with the electronic ground state has been identified. Close to the conical intersection, the six-membered ring of adenine is strongly puckered and the electronic structure of the S(1) state corresponds to a pi-->pi* excitation. The energetic accessibility of this relaxation path at about 0.1 eV above the singlet n-->pi* minimum is presumably responsible for the ultrafast decay of 9H-adenine after photoexcitation and explains why sharp vibronic peaks can only be observed in a rather narrow wavelength range above the origin. The detected mechanism should be equally applicable to adenosine and 9-methyladenine because it involves primarily geometry changes in the six-membered ring whereas the nuclear arrangement of the five-membered ring (including the N(9) center) is largely preserved.

Computation of conical intersections by using perturbation techniques

Multiconfigurational second-order perturbation theory, both in its single-state multiconfigurational second-order perturbation theory (CASPT2) and multistate (MS-CASPT2) formulations, is used to search for minima on the crossing seams between different potential energy hypersurfaces of electronic states in several molecular systems. The performance of the procedures is tested and discussed, focusing on the problem of the nonorthogonality of the single-state perturbative solutions. In different cases the obtained structures and energy differences are compared with available complete active space self-consistent field and multireference configuration interaction solutions. Calculations on different state crossings in LiF, formaldehyde, the ethene dimer, and the penta-2,4-dieniminium cation illustrate the discussions. Practical procedures to validate the CASPT2 solutions in polyatomic systems are explored, while it is shown that the application of the MS-CASPT2 procedure is not straightforward and requires a careful analysis of the stability of the results with the quality of the reference wave functions, that is, the size of the active space.

First Principle Computational Study on the Full Conformational Space of l-Proline Diamides

Ab initio molecular orbital computations were carried out at three levels of theory: RHF/3-21G, RHF/6-31G(d), and B3LYP/6-31G(d), on four model systems of the amino acid proline, HCO-Pro-NH2 [I], HCO-Pro-NH-Me [II], MeCO-Pro-NH2 [III], and MeCO-Pro-NH-Me [IV], representing a systematic variation in the protecting N- and C-terminal groups. Three previously located backbone conformations, gammaL, epsilonL, and alphaL, were characterized together with two ring-puckered forms syn (gauche+ = g+) or "DOWN" and anti (gauche- = g-) or "UP", as well as trans-trans, trans-cis, cis-trans, and cis-cis peptide bond isomers. The topologies of the conformational potential energy cross-sections (PECS) of the potential energy hypersurfaces (PEHS) for compounds [I]-[IV] were explored and analyzed in terms of potential energy curves (PEC), and HCO-Pro-NH2 [I] was also analyzed in terms of potential energy surfaces (PESs). Thermodynamic functions were also calculated for HCO-Pro-NH2 [I] at the CBS-4M and G3MP2 levels of theory. The study confirms that the use of the simplest model, compound [I] with P(N) = P(C) = H, along with the RHF/3-21G level of theory, is an acceptable practice for the analysis of peptide models because only minor differences in geometry and stability are observed.

The Ratio Dint /D between the Coefficients for the Diffusion of Internal Energy and of Self Diffusion in Thermal Conductivity Data Correlations for Gases of Linear Molecules

Highly consistent sets of generalized cross sections are used to judge critically correlations of the thermal conductivity in the limit of zero density for nitrogen, carbon monoxide, and carbon dioxide. The correlations were developed by Millat, Vesovic, and Wakeham some years ago using restricted experimental information in order to deduce a set of generalized cross sections as consistent as possible for the extrapolation beyond the temperature range of the primary experimental data. Recently, the generalized cross sections needed have been evaluated by means of classical trajectory calculations for rigid rotors on the basis of accurate anisotropic ah initio potential energy hypersurfaces including a new improved way to take into account the vibrational degrees of freedom. It is shown that the ratio between the coefficients of internal energy and of self diffusion D i n t /D was not appropriately chosen and that this effect was extensively compensated in a fortuitous way in the course of the development of the data correlations by a likewise unsuitable choice of the ratio A* between the effective cross sections of viscosity and self-diffusion.

Static and dynamics mapping of energy landscape in potassium-silicate glass structure

The structure of 5K2O·85SiO2 (K05) and 15K2O·75SiO2 (K15) glasses were obtained with help of molecular dynamics method. The relation between the glass structure in the vicinity of potassium ions and the potential-energy hypersurface was studied by means of the static and the dynamic approaches. The energy maps of ions in open and closed sites are presented up to 3.5Å. Calculated activation energy distributions were compared for case of static and dynamic approaches and both glasses. The dynamic approach significantly decreased the activation energy due to the enabled relaxation of the surrounding glass. However, due to the neglecting of correlations in potassium transport the mean activation energy of potassium is still higher in glass with higher alkali content (K15).

Stochastic strategy to analyze protein folding

We propose a stochastic approach to combine methods from computational physics and Tsallis statistics in order to analyze the potential energy hypersurface of the proteins. This approach enables us to study protein folding by the topology of the energy hypersurface close to the native structures. As a bonus, this stochastic procedure allows us to obtain some of the possible intermediate states of protein folding. In particular, we describe results which suggest that the enthalpy drives the process of protein folding close to the native state. Finally, we propose an alternative view of the process of protein folding.

Ab initio potential-energy surfaces for complex, multichannel systems using modified novelty sampling and feedforward neural networks

A neural network/trajectory approach is presented for the development of accurate potential-energy hypersurfaces that can be utilized to conduct ab initio molecular dynamics (AIMD) and Monte Carlo studies of gas-phase chemical reactions, nanometric cutting, and nanotribology, and of a variety of mechanical properties of importance in potential microelectromechanical systems applications. The method is sufficiently robust that it can be applied to a wide range of polyatomic systems. The overall method integrates ab initio electronic structure calculations with importance sampling techniques that permit the critical regions of configuration space to be determined. The computed ab initio energies and gradients are then accurately interpolated using neural networks (NN) rather than arbitrary parametrized analytical functional forms, moving interpolation or least-squares methods. The sampling method involves a tight integration of molecular dynamics calculations with neural networks that employ early stopping and regularization procedures to improve network performance and test for convergence. The procedure can be initiated using an empirical potential surface or direct dynamics. The accuracy and interpolation power of the method has been tested for two cases, the global potential surface for vinyl bromide undergoing unimolecular decomposition via four different reaction channels and nanometric cutting of silicon. The results show that the sampling methods permit the important regions of configuration space to be easily and rapidly identified, that convergence of the NN fit to the ab initio electronic structure database can be easily monitored, and that the interpolation accuracy of the NN fits is excellent, even for systems involving five atoms or more. The method permits a substantial computational speed and accuracy advantage over existing methods, is robust, and relatively easy to implement.

Density functional theory study of the hydrogen bonding interaction of the dimers of formylhalide

The hydrogen bonding of the dimers of formylhalide has been completely investigated in the present study using density functional theory (DFT), HF and second-order Moller–Plesset Perturbation (MP2) methods with the 6-311++g(d,p) basis set. Four reasonable geometries on the potential energy hypersurface of the dimers of formylhalide system are considered with the global minimum being a cyclic double-hydrogen bonded structure. The optimized geometric parameters and interaction energies for various isomers are estimated. The infrared spectrum frequencies, IR intensities and the vibrational frequency shifts are reported.

Conformational study of internally retrograde and quasi-retrograde molecules — An ab initio and DFT study

A conformational study of the symmetrical and nonsymmetrical homologue series was carried out. In this study, ab initio (RHF/3-21G and RHF/6-31G(d)) and density functional theory (B3LYP/6-31G(d)) calculations were performed. The presence of two symmetrical aromatic systems (identical or not) reduces notably the conformational possibilities of these compounds. Our results indicate that RHF/3-21G calculations are sufficient to use in a preliminary form. However, from our results it is prudent to use this technique only for a preliminary or exploratory conformational analysis. Thus, at least, the HF level of theory in conjunction with more extended basis sets and the inclusion of electron correlation appear to be necessary to confirm critical points at the potential energy hyper surfaces (PEHSs) and to assign the conformational preferences of these compounds. In the present paper, we report a complete and comprehensive picture of the conformational intricacies of the compounds with a small flexible connecting chain (n = 1–5). In addition, an "educated guess" for the conformational behaviour of large-size homologues (n = 6–10) is also reported.Key words: ab initio and DFT calculations, conformational study, homologue series.

Berry phase and entanglement in the icosahedralH⊗(g⊕2h)Jahn-Teller system with trigonal minima

The $H\ensuremath{\bigotimes}(g\ensuremath{\bigoplus}2h)$ Jahn-Teller problem in the trigonal regime offers an example of a dynamic ground-state crossover from a degenerate to a singlet state. This crossover is connected to a change in tunneling paths which results in a loss of Berry phase. Previous studies tried to explain the entanglement which lies at the basis of this phenomenon using two-dimensional (2D) cuts through coordinate space but have reached opposite interpretations. In this paper we introduce a method which scans the topology of the full coordinate space using a net of triangular cross sections between the ten ${D}_{3d}$ minima. It is shown that the Berry phase of every loop on the potential energy hypersurface can be expressed in terms of these 2D triangular cross sections. Using this method we show that the absence of Berry phase for the cycles containing five trigonal wells originates from two seams of conical intersections going through these cycles. The connection between this analysis and previous treatments is established and the apparent dilemma of interpretation is resolved.

Theoretical study of helical structure and chiral discrimination of cysteine dimer

The helical structure and chiral discrimination of cysteine dimer have been completely investigated in the present study using density functional theory method B3LYP at the 6-31G level. Three reasonable geometries on the potential energy hypersurface of the cysteine–cysteine system are considered with the global minimum. The optimized geometric parameters and interaction energies for various isomers at the 6-31G level are estimated.

An Exhaustive Conformational Analysis ofN-Acetyl-l-cysteine-N-methylamide. Identification of the Complete Set of Interconversion Pathways on the ab Initio and DFT Potential Energy Hypersurface

The full conformational space of N-acetyl-l-cysteine-N-methylamide was explored by ab initio (RHF/ 6-31G(d)) and DFT (B3LYP/6-31G(d)) computations. Multidimensional conformational analysis predicts 81 structures in N-acetyl-l-cysteine-N-methylamide, but only 47 relaxed structures were previously determined at the RHF/3-21G level of theory. These structures were now optimized using RHF/6-31G(d) and B3LYP/6-31G(d) approaches. Seven conformational migrations were observed when recalculated at higher level of theory. Besides these major changes, only smaller conformational shifts were operative for the remaining stationary points. The exploration of the whole conformational space of N-acetyl-l-cysteine-N-methylamide, including the transition-state structures allowing the conformational interconversion among the low-energy forms, was analyzed in this study. Our results offer new insights into the influence of polar side chains on the conformational preferences of peptide structures.

Coverage dependence of oxygen decomposition and surface diffusion on rhodium (111): A DFT study

A systematic study of oxygen adsorption, decomposition and diffusion on Rh111 and its dependence on coadsorbed oxygen molecules has been performed using density functional theory calculations. First, the bonding strength between metal surface and adsorbed oxygen molecules has been studied as a function of initial oxygen coverage. The bonding strength decreases with increasing oxygen coverage, which points towards a self-inhibition of the adsorption process. The potential energy hypersurface (PES) for the dissociation of oxygen molecules adsorbed on a threefold fcc position perpendicular to the surface was calculated using a combined linear/quadratic synchronous transit method with conjugate gradient refinements. The results indicate that a minor amount of oxygen on the surface enhances the decomposition of further oxygen molecules, while this process is inhibited at higher coverage. Moreover, PES calculations of a single site jump of atomic oxygen on rhodium 111 indicate that the activation energy increases as well with increasing oxygen coverage. All results are discussed with respect to a rhodium based catalytic NOx reduction/decomposition system proposed by Nakatsuji, which decomposes nitrogen oxides in oxygen excess.

Density functional theory study of the hydrogen bonding interaction of 1:1 complexes of serine with water

AbstractThe hydrogen bonding of 1:1 complexes formed between serine and water molecules were completely investigated in the present study employing ab initio and Density Functional Theory (DFT) methods at varied basis set levels from 6‐31g to 6‐311++g (2d,2p). For comparison, we also used the second‐order Moller–Plesset Perturbation (MP2) method at the 6‐31+g(d) level. Twelve reasonable geometries on the potential energy hypersurface of serine and water system were considered with the global minimum, 10 of which are cyclic double‐hydrogen bonded structures and the other two are one‐hydrogen bonded structures. The optimized geometric parameters and interaction energies for various isomers at different levels were estimated. The infrared spectrum frequencies, IR intensities, and the vibrational frequency shifts are reported. Finally, the solvent effects on the geometries of the serine–water complexes were also investigated using self‐consistent reaction‐field (SCRF) calculations at the B3LYP/6‐311++g(d,p) level. The results indicate that the polarity of the solvent played an important role in the structures and relative stabilities of different isomers. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005